#########################################################
# 1. Download data from NCBI using SRA Toolkit
#########################################################
./fastq-dump ../SRA/SRR805390/SRR805390.sra&
./fastq-dump ../SRA/SRR805391/SRR805391.sra&
./fastq-dump ../SRA/SRR805392/SRR805392.sra&
./fastq-dump ../SRA/SRR805393/SRR805393.sra&
./fastq-dump ../SRA/SRR805394/SRR805394.sra&
./fastq-dump ../SRA/SRR805395/SRR805395.sra&
./fastq-dump ../SRA/SRR805396/SRR805396.sra&
./fastq-dump ../SRA/SRR805397/SRR805397.sra&
./fastq-dump ../SRA/SRR805398/SRR805398.sra&
./fastq-dump ../SRA/SRR805399/SRR805399.sra&
./fastq-dump ../SRA/SRR805400/SRR805400.sra&
./fastq-dump ../SRA/SRR805401/SRR805401.sra&
./fastq-dump ../SRA/SRR805402/SRR805402.sra&
./fastq-dump ../SRA/SRR805403/SRR805403.sra&
./fastq-dump ../SRA/SRR805404/SRR805404.sra&
./fastq-dump ../SRA/SRR805405/SRR805405.sra&
./fastq-dump ../SRA/SRR805406/SRR805406.sra&
./fastq-dump ../SRA/SRR805407/SRR805407.sra&
./fastq-dump ../SRA/SRR805408/SRR805408.sra&
./fastq-dump ../SRA/SRR805409/SRR805409.sra&
./fastq-dump ../SRA/SRR805410/SRR805410.sra&
./fastq-dump ../SRA/SRR805411/SRR805411.sra&
./fastq-dump ../SRA/SRR805412/SRR805412.sra&
./fastq-dump ../SRA/SRR805413/SRR805413.sra&
./fastq-dump ../SRA/SRR805414/SRR805414.sra&
./fastq-dump ../SRA/SRR805415/SRR805415.sra&
./fastq-dump ../SRA/SRR805416/SRR805416.sra&
./fastq-dump ../SRA/SRR805417/SRR805417.sra&
./fastq-dump ../SRA/SRR805418/SRR805418.sra&
./fastq-dump ../SRA/SRR805419/SRR805419.sra
./fastq-dump ../SRA/SRR805420/SRR805420.sra&
./fastq-dump ../SRA/SRR805421/SRR805421.sra&
./fastq-dump ../SRA/SRR805422/SRR805422.sra&
./fastq-dump ../SRA/SRR805423/SRR805423.sra&
./fastq-dump ../SRA/SRR805424/SRR805424.sra&
./fastq-dump ../SRA/SRR805425/SRR805425.sra&
./fastq-dump ../SRA/SRR805426/SRR805426.sra&
./fastq-dump ../SRA/SRR805427/SRR805427.sra&
./fastq-dump ../SRA/SRR805428/SRR805428.sra&
./fastq-dump ../SRA/SRR805429/SRR805429.sra&
./fastq-dump ../SRA/SRR805430/SRR805430.sra&
./fastq-dump ../SRA/SRR805431/SRR805431.sra&
./fastq-dump ../SRA/SRR805432/SRR805432.sra&
./fastq-dump ../SRA/SRR805433/SRR805433.sra&
./fastq-dump ../SRA/SRR805434/SRR805434.sra&
./fastq-dump ../SRA/SRR805435/SRR805435.sra&
./fastq-dump ../SRA/SRR805436/SRR805436.sra&
./fastq-dump ../SRA/SRR805437/SRR805437.sra&
./fastq-dump ../SRA/SRR805438/SRR805438.sra&
./fastq-dump ../SRA/SRR805439/SRR805439.sra&
./fastq-dump ../SRA/SRR805440/SRR805440.sra&
./fastq-dump ../SRA/SRR805441/SRR805441.sra&
./fastq-dump ../SRA/SRR805442/SRR805442.sra&
./fastq-dump ../SRA/SRR805443/SRR805443.sra&
./fastq-dump ../SRA/SRR805444/SRR805444.sra&
./fastq-dump ../SRA/SRR805445/SRR805445.sra&
./fastq-dump ../SRA/SRR805446/SRR805446.sra&
./fastq-dump ../SRA/SRR805447/SRR805447.sra&
./fastq-dump ../SRA/SRR805448/SRR805448.sra&
./fastq-dump ../SRA/SRR805449/SRR805449.sra
./fastq-dump ../SRA/SRR805450/SRR805450.sra&
./fastq-dump ../SRA/SRR805451/SRR805451.sra&
./fastq-dump ../SRA/SRR805452/SRR805452.sra&
./fastq-dump ../SRA/SRR1041728/SRR1041728.sra&
./fastq-dump ../SRA/SRR1041729/SRR1041729.sra&
./fastq-dump ../SRA/SRR1041730/SRR1041730.sra&
./fastq-dump ../SRA/SRR1041731/SRR1041731.sra&
./fastq-dump ../SRA/SRR1041732/SRR1041732.sra&
./fastq-dump ../SRA/SRR1041733/SRR1041733.sra&
./fastq-dump ../SRA/SRR1041734/SRR1041734.sra&
./fastq-dump ../SRA/SRR1041735/SRR1041735.sra&
./fastq-dump ../SRA/SRR1041736/SRR1041736.sra&
./fastq-dump ../SRA/SRR1041737/SRR1041737.sra&
./fastq-dump ../SRA/SRR1041738/SRR1041738.sra&
./fastq-dump ../SRA/SRR1041739/SRR1041739.sra&
./fastq-dump ../SRA/SRR1041740/SRR1041740.sra&
./fastq-dump ../SRA/SRR1041741/SRR1041741.sra&
./fastq-dump ../SRA/SRR1041742/SRR1041742.sra&
./fastq-dump ../SRA/SRR1041743/SRR1041743.sra&
./fastq-dump ../SRA/SRR1041744/SRR1041744.sra&
./fastq-dump ../SRA/SRR1041745/SRR1041745.sra&
./fastq-dump ../SRA/SRR1041746/SRR1041746.sra&
./fastq-dump ../SRA/SRR1041747/SRR1041747.sra&
./fastq-dump ../SRA/SRR1041748/SRR1041748.sra&
./fastq-dump ../SRA/SRR1041749/SRR1041749.sra&
./fastq-dump ../SRA/SRR1041750/SRR1041750.sra&
./fastq-dump ../SRA/SRR1041751/SRR1041751.sra&
./fastq-dump ../SRA/SRR1041752/SRR1041752.sra&
./fastq-dump ../SRA/SRR1041753/SRR1041753.sra&
./fastq-dump ../SRA/SRR1041754/SRR1041754.sra
./fastq-dump ../SRA/SRR1041755/SRR1041755.sra&
./fastq-dump ../SRA/SRR1041756/SRR1041756.sra&
./fastq-dump ../SRA/SRR1041757/SRR1041757.sra&
./fastq-dump ../SRA/SRR1041758/SRR1041758.sra&
./fastq-dump ../SRA/SRR1041759/SRR1041759.sra&
./fastq-dump ../SRA/SRR1041760/SRR1041760.sra&
./fastq-dump ../SRA/SRR1041761/SRR1041761.sra&
./fastq-dump ../SRA/SRR1041762/SRR1041762.sra&
./fastq-dump ../SRA/SRR1041763/SRR1041763.sra&
./fastq-dump ../SRA/SRR1041764/SRR1041764.sra&
./fastq-dump ../SRA/SRR805290/SRR805290.sra&
./fastq-dump ../SRA/SRR805291/SRR805291.sra&
./fastq-dump ../SRA/SRR805292/SRR805292.sra&
./fastq-dump ../SRA/SRR805293/SRR805293.sra&
./fastq-dump ../SRA/SRR805294/SRR805294.sra&
./fastq-dump ../SRA/SRR805295/SRR805295.sra&
./fastq-dump ../SRA/SRR805296/SRR805296.sra&
./fastq-dump ../SRA/SRR805297/SRR805297.sra&
./fastq-dump ../SRA/SRR805298/SRR805298.sra&
./fastq-dump ../SRA/SRR805299/SRR805299.sra&
./fastq-dump ../SRA/SRR805300/SRR805300.sra&
./fastq-dump ../SRA/SRR805301/SRR805301.sra&
./fastq-dump ../SRA/SRR805302/SRR805302.sra&
./fastq-dump ../SRA/SRR805303/SRR805303.sra&
./fastq-dump ../SRA/SRR805304/SRR805304.sra&
./fastq-dump ../SRA/SRR805305/SRR805305.sra&
./fastq-dump ../SRA/SRR805306/SRR805306.sra&
./fastq-dump ../SRA/SRR805307/SRR805307.sra&
./fastq-dump ../SRA/SRR805308/SRR805308.sra&
./fastq-dump ../SRA/SRR805309/SRR805309.sra
./fastq-dump ../SRA/SRR805310/SRR805310.sra&
./fastq-dump ../SRA/SRR805311/SRR805311.sra&
./fastq-dump ../SRA/SRR805312/SRR805312.sra&
./fastq-dump ../SRA/SRR805313/SRR805313.sra&
./fastq-dump ../SRA/SRR805314/SRR805314.sra&
./fastq-dump ../SRA/SRR805315/SRR805315.sra&
./fastq-dump ../SRA/SRR805316/SRR805316.sra&
./fastq-dump ../SRA/SRR805317/SRR805317.sra&
./fastq-dump ../SRA/SRR805318/SRR805318.sra&
./fastq-dump ../SRA/SRR805319/SRR805319.sra&
./fastq-dump ../SRA/SRR805320/SRR805320.sra&
./fastq-dump ../SRA/SRR805321/SRR805321.sra&
./fastq-dump ../SRA/SRR805322/SRR805322.sra&
./fastq-dump ../SRA/SRR805323/SRR805323.sra&
./fastq-dump ../SRA/SRR805324/SRR805324.sra&
./fastq-dump ../SRA/SRR805325/SRR805325.sra&
./fastq-dump ../SRA/SRR805326/SRR805326.sra&
./fastq-dump ../SRA/SRR805327/SRR805327.sra&
./fastq-dump ../SRA/SRR805328/SRR805328.sra&
./fastq-dump ../SRA/SRR805329/SRR805329.sra&
./fastq-dump ../SRA/SRR805330/SRR805330.sra&
./fastq-dump ../SRA/SRR805331/SRR805331.sra&
./fastq-dump ../SRA/SRR805332/SRR805332.sra&
./fastq-dump ../SRA/SRR805333/SRR805333.sra&
./fastq-dump ../SRA/SRR805334/SRR805334.sra&
./fastq-dump ../SRA/SRR805335/SRR805335.sra&
./fastq-dump ../SRA/SRR805336/SRR805336.sra&
./fastq-dump ../SRA/SRR805337/SRR805337.sra&
./fastq-dump ../SRA/SRR805338/SRR805338.sra&
./fastq-dump ../SRA/SRR805339/SRR805339.sra
./fastq-dump ../SRA/SRR805340/SRR805340.sra&
./fastq-dump ../SRA/SRR805341/SRR805341.sra&
./fastq-dump ../SRA/SRR805342/SRR805342.sra&
./fastq-dump ../SRA/SRR805343/SRR805343.sra&
./fastq-dump ../SRA/SRR805344/SRR805344.sra&
./fastq-dump ../SRA/SRR805345/SRR805345.sra&
./fastq-dump ../SRA/SRR805346/SRR805346.sra&
./fastq-dump ../SRA/SRR805347/SRR805347.sra&
./fastq-dump ../SRA/SRR805348/SRR805348.sra&
./fastq-dump ../SRA/SRR805349/SRR805349.sra&
./fastq-dump ../SRA/SRR805350/SRR805350.sra&
./fastq-dump ../SRA/SRR805351/SRR805351.sra&
./fastq-dump ../SRA/SRR805352/SRR805352.sra&
./fastq-dump ../SRA/SRR805353/SRR805353.sra&
./fastq-dump ../SRA/SRR805354/SRR805354.sra&
./fastq-dump ../SRA/SRR805355/SRR805355.sra&
./fastq-dump ../SRA/SRR805356/SRR805356.sra&
./fastq-dump ../SRA/SRR805357/SRR805357.sra&
./fastq-dump ../SRA/SRR805358/SRR805358.sra&
./fastq-dump ../SRA/SRR805359/SRR805359.sra&
./fastq-dump ../SRA/SRR805360/SRR805360.sra&
./fastq-dump ../SRA/SRR805361/SRR805361.sra&
./fastq-dump ../SRA/SRR805362/SRR805362.sra&
./fastq-dump ../SRA/SRR805363/SRR805363.sra&
./fastq-dump ../SRA/SRR805364/SRR805364.sra&
./fastq-dump ../SRA/SRR805365/SRR805365.sra&
./fastq-dump ../SRA/SRR805366/SRR805366.sra&
./fastq-dump ../SRA/SRR805367/SRR805367.sra&
./fastq-dump ../SRA/SRR805368/SRR805368.sra&
./fastq-dump ../SRA/SRR805369/SRR805369.sra
./fastq-dump ../SRA/SRR805370/SRR805370.sra&
./fastq-dump ../SRA/SRR805371/SRR805371.sra&
./fastq-dump ../SRA/SRR805372/SRR805372.sra&
./fastq-dump ../SRA/SRR805373/SRR805373.sra&
./fastq-dump ../SRA/SRR805374/SRR805374.sra&
./fastq-dump ../SRA/SRR805375/SRR805375.sra&
./fastq-dump ../SRA/SRR805376/SRR805376.sra&
./fastq-dump ../SRA/SRR805377/SRR805377.sra&
./fastq-dump ../SRA/SRR805378/SRR805378.sra&
./fastq-dump ../SRA/SRR805379/SRR805379.sra&
./fastq-dump ../SRA/SRR805380/SRR805380.sra&
./fastq-dump ../SRA/SRR805381/SRR805381.sra&
./fastq-dump ../SRA/SRR805382/SRR805382.sra&
./fastq-dump ../SRA/SRR805383/SRR805383.sra&
./fastq-dump ../SRA/SRR805384/SRR805384.sra&
./fastq-dump ../SRA/SRR805385/SRR805385.sra&
./fastq-dump ../SRA/SRR805386/SRR805386.sra&
./fastq-dump ../SRA/SRR805387/SRR805387.sra&
./fastq-dump ../SRA/SRR805388/SRR805388.sra&
./fastq-dump ../SRA/SRR805389/SRR805389.sra&
./fastq-dump ../SRA/SRR805190/SRR805190.sra&
./fastq-dump ../SRA/SRR805191/SRR805191.sra&
./fastq-dump ../SRA/SRR805192/SRR805192.sra&
./fastq-dump ../SRA/SRR805193/SRR805193.sra&
./fastq-dump ../SRA/SRR805194/SRR805194.sra&
./fastq-dump ../SRA/SRR805195/SRR805195.sra&
./fastq-dump ../SRA/SRR805196/SRR805196.sra&
./fastq-dump ../SRA/SRR805197/SRR805197.sra&
./fastq-dump ../SRA/SRR805198/SRR805198.sra&
./fastq-dump ../SRA/SRR805199/SRR805199.sra
./fastq-dump ../SRA/SRR805200/SRR805200.sra&
./fastq-dump ../SRA/SRR805201/SRR805201.sra&
./fastq-dump ../SRA/SRR805202/SRR805202.sra&
./fastq-dump ../SRA/SRR805203/SRR805203.sra&
./fastq-dump ../SRA/SRR805204/SRR805204.sra&
./fastq-dump ../SRA/SRR805205/SRR805205.sra&
./fastq-dump ../SRA/SRR805206/SRR805206.sra&
./fastq-dump ../SRA/SRR805207/SRR805207.sra&
./fastq-dump ../SRA/SRR805208/SRR805208.sra&
./fastq-dump ../SRA/SRR805209/SRR805209.sra&
./fastq-dump ../SRA/SRR805210/SRR805210.sra&
./fastq-dump ../SRA/SRR805211/SRR805211.sra&
./fastq-dump ../SRA/SRR805212/SRR805212.sra&
./fastq-dump ../SRA/SRR805213/SRR805213.sra&
./fastq-dump ../SRA/SRR805214/SRR805214.sra&
./fastq-dump ../SRA/SRR805215/SRR805215.sra&
./fastq-dump ../SRA/SRR805216/SRR805216.sra&
./fastq-dump ../SRA/SRR805217/SRR805217.sra&
./fastq-dump ../SRA/SRR805218/SRR805218.sra&
./fastq-dump ../SRA/SRR805219/SRR805219.sra&
./fastq-dump ../SRA/SRR805220/SRR805220.sra&
./fastq-dump ../SRA/SRR805221/SRR805221.sra&
./fastq-dump ../SRA/SRR805222/SRR805222.sra&
./fastq-dump ../SRA/SRR805223/SRR805223.sra&
./fastq-dump ../SRA/SRR805224/SRR805224.sra&
./fastq-dump ../SRA/SRR805225/SRR805225.sra&
./fastq-dump ../SRA/SRR805226/SRR805226.sra&
./fastq-dump ../SRA/SRR805227/SRR805227.sra&
./fastq-dump ../SRA/SRR805228/SRR805228.sra&
./fastq-dump ../SRA/SRR805229/SRR805229.sra
./fastq-dump ../SRA/SRR805230/SRR805230.sra&
./fastq-dump ../SRA/SRR805231/SRR805231.sra&
./fastq-dump ../SRA/SRR805232/SRR805232.sra&
./fastq-dump ../SRA/SRR805233/SRR805233.sra&
./fastq-dump ../SRA/SRR805234/SRR805234.sra&
./fastq-dump ../SRA/SRR805235/SRR805235.sra&
./fastq-dump ../SRA/SRR805236/SRR805236.sra&
./fastq-dump ../SRA/SRR805237/SRR805237.sra&
./fastq-dump ../SRA/SRR805238/SRR805238.sra&
./fastq-dump ../SRA/SRR805239/SRR805239.sra&
./fastq-dump ../SRA/SRR805240/SRR805240.sra&
./fastq-dump ../SRA/SRR805241/SRR805241.sra&
./fastq-dump ../SRA/SRR805242/SRR805242.sra&
./fastq-dump ../SRA/SRR805243/SRR805243.sra&
./fastq-dump ../SRA/SRR805244/SRR805244.sra&
./fastq-dump ../SRA/SRR805245/SRR805245.sra&
./fastq-dump ../SRA/SRR805246/SRR805246.sra&
./fastq-dump ../SRA/SRR805247/SRR805247.sra&
./fastq-dump ../SRA/SRR805248/SRR805248.sra&
./fastq-dump ../SRA/SRR805249/SRR805249.sra&
./fastq-dump ../SRA/SRR805250/SRR805250.sra&
./fastq-dump ../SRA/SRR805251/SRR805251.sra&
./fastq-dump ../SRA/SRR805252/SRR805252.sra&
./fastq-dump ../SRA/SRR805253/SRR805253.sra&
./fastq-dump ../SRA/SRR805254/SRR805254.sra&
./fastq-dump ../SRA/SRR805255/SRR805255.sra&
./fastq-dump ../SRA/SRR805256/SRR805256.sra&
./fastq-dump ../SRA/SRR805257/SRR805257.sra&
./fastq-dump ../SRA/SRR805258/SRR805258.sra&
./fastq-dump ../SRA/SRR805259/SRR805259.sra
./fastq-dump ../SRA/SRR805260/SRR805260.sra&
./fastq-dump ../SRA/SRR805261/SRR805261.sra&
./fastq-dump ../SRA/SRR805262/SRR805262.sra&
./fastq-dump ../SRA/SRR805263/SRR805263.sra&
./fastq-dump ../SRA/SRR805264/SRR805264.sra&
./fastq-dump ../SRA/SRR805265/SRR805265.sra&
./fastq-dump ../SRA/SRR805266/SRR805266.sra&
./fastq-dump ../SRA/SRR805267/SRR805267.sra&
./fastq-dump ../SRA/SRR805268/SRR805268.sra&
./fastq-dump ../SRA/SRR805269/SRR805269.sra&
./fastq-dump ../SRA/SRR805270/SRR805270.sra&
./fastq-dump ../SRA/SRR805271/SRR805271.sra&
./fastq-dump ../SRA/SRR805272/SRR805272.sra&
./fastq-dump ../SRA/SRR805273/SRR805273.sra&
./fastq-dump ../SRA/SRR805274/SRR805274.sra&
./fastq-dump ../SRA/SRR805275/SRR805275.sra&
./fastq-dump ../SRA/SRR805276/SRR805276.sra&
./fastq-dump ../SRA/SRR805277/SRR805277.sra&
./fastq-dump ../SRA/SRR805278/SRR805278.sra&
./fastq-dump ../SRA/SRR805279/SRR805279.sra&
./fastq-dump ../SRA/SRR805280/SRR805280.sra&
./fastq-dump ../SRA/SRR805281/SRR805281.sra&
./fastq-dump ../SRA/SRR805282/SRR805282.sra&
./fastq-dump ../SRA/SRR805283/SRR805283.sra&
./fastq-dump ../SRA/SRR805284/SRR805284.sra&
./fastq-dump ../SRA/SRR805285/SRR805285.sra&
./fastq-dump ../SRA/SRR805286/SRR805286.sra&
./fastq-dump ../SRA/SRR805287/SRR805287.sra&
./fastq-dump ../SRA/SRR805288/SRR805288.sra&
./fastq-dump ../SRA/SRR805289/SRR805289.sra
./fastq-dump ../SRA/SRR805173/SRR805173.sra&
./fastq-dump ../SRA/SRR805174/SRR805174.sra&
./fastq-dump ../SRA/SRR805175/SRR805175.sra&
./fastq-dump ../SRA/SRR805176/SRR805176.sra&
./fastq-dump ../SRA/SRR805177/SRR805177.sra&
./fastq-dump ../SRA/SRR805178/SRR805178.sra&
./fastq-dump ../SRA/SRR805179/SRR805179.sra&
./fastq-dump ../SRA/SRR805180/SRR805180.sra&
./fastq-dump ../SRA/SRR805181/SRR805181.sra&
./fastq-dump ../SRA/SRR805182/SRR805182.sra&
./fastq-dump ../SRA/SRR805183/SRR805183.sra&
./fastq-dump ../SRA/SRR805184/SRR805184.sra&
./fastq-dump ../SRA/SRR805185/SRR805185.sra&
./fastq-dump ../SRA/SRR805186/SRR805186.sra&
./fastq-dump ../SRA/SRR805187/SRR805187.sra&
./fastq-dump ../SRA/SRR805188/SRR805188.sra&
./fastq-dump ../SRA/SRR805189/SRR805189.sra&

##########################################################
2. Adaptor trimming using cutadapt
##########################################################

/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805372-trimmed.fastq ../fastq/SRR805372.fastq > reports_SRR805372&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805373-trimmed.fastq ../fastq/SRR805373.fastq > reports_SRR805373&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805374-trimmed.fastq ../fastq/SRR805374.fastq > reports_SRR805374&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805375-trimmed.fastq ../fastq/SRR805375.fastq > reports_SRR805375&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805376-trimmed.fastq ../fastq/SRR805376.fastq > reports_SRR805376&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805377-trimmed.fastq ../fastq/SRR805377.fastq > reports_SRR805377&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805378-trimmed.fastq ../fastq/SRR805378.fastq > reports_SRR805378&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805379-trimmed.fastq ../fastq/SRR805379.fastq > reports_SRR805379&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805380-trimmed.fastq ../fastq/SRR805380.fastq > reports_SRR805380&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805381-trimmed.fastq ../fastq/SRR805381.fastq > reports_SRR805381&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805382-trimmed.fastq ../fastq/SRR805382.fastq > reports_SRR805382&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805383-trimmed.fastq ../fastq/SRR805383.fastq > reports_SRR805383&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805384-trimmed.fastq ../fastq/SRR805384.fastq > reports_SRR805384&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805385-trimmed.fastq ../fastq/SRR805385.fastq > reports_SRR805385&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805386-trimmed.fastq ../fastq/SRR805386.fastq > reports_SRR805386&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805387-trimmed.fastq ../fastq/SRR805387.fastq > reports_SRR805387&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805388-trimmed.fastq ../fastq/SRR805388.fastq > reports_SRR805388&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805389-trimmed.fastq ../fastq/SRR805389.fastq > reports_SRR805389&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805190-trimmed.fastq ../fastq/SRR805190.fastq > reports_SRR805190&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805191-trimmed.fastq ../fastq/SRR805191.fastq > reports_SRR805191&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805192-trimmed.fastq ../fastq/SRR805192.fastq > reports_SRR805192&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805193-trimmed.fastq ../fastq/SRR805193.fastq > reports_SRR805193&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805194-trimmed.fastq ../fastq/SRR805194.fastq > reports_SRR805194&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805195-trimmed.fastq ../fastq/SRR805195.fastq > reports_SRR805195&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805196-trimmed.fastq ../fastq/SRR805196.fastq > reports_SRR805196&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805197-trimmed.fastq ../fastq/SRR805197.fastq > reports_SRR805197&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805198-trimmed.fastq ../fastq/SRR805198.fastq > reports_SRR805198&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805199-trimmed.fastq ../fastq/SRR805199.fastq > reports_SRR805199&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805200-trimmed.fastq ../fastq/SRR805200.fastq > reports_SRR805200&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805201-trimmed.fastq ../fastq/SRR805201.fastq > reports_SRR805201&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805202-trimmed.fastq ../fastq/SRR805202.fastq > reports_SRR805202&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805203-trimmed.fastq ../fastq/SRR805203.fastq > reports_SRR805203&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805204-trimmed.fastq ../fastq/SRR805204.fastq > reports_SRR805204&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805205-trimmed.fastq ../fastq/SRR805205.fastq > reports_SRR805205&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805206-trimmed.fastq ../fastq/SRR805206.fastq > reports_SRR805206&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805207-trimmed.fastq ../fastq/SRR805207.fastq > reports_SRR805207&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805208-trimmed.fastq ../fastq/SRR805208.fastq > reports_SRR805208&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805209-trimmed.fastq ../fastq/SRR805209.fastq > reports_SRR805209&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805210-trimmed.fastq ../fastq/SRR805210.fastq > reports_SRR805210&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805211-trimmed.fastq ../fastq/SRR805211.fastq > reports_SRR805211&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805212-trimmed.fastq ../fastq/SRR805212.fastq > reports_SRR805212&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805213-trimmed.fastq ../fastq/SRR805213.fastq > reports_SRR805213&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805214-trimmed.fastq ../fastq/SRR805214.fastq > reports_SRR805214&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805215-trimmed.fastq ../fastq/SRR805215.fastq > reports_SRR805215&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805216-trimmed.fastq ../fastq/SRR805216.fastq > reports_SRR805216&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805217-trimmed.fastq ../fastq/SRR805217.fastq > reports_SRR805217&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805218-trimmed.fastq ../fastq/SRR805218.fastq > reports_SRR805218&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805219-trimmed.fastq ../fastq/SRR805219.fastq > reports_SRR805219&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805220-trimmed.fastq ../fastq/SRR805220.fastq > reports_SRR805220&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805221-trimmed.fastq ../fastq/SRR805221.fastq > reports_SRR805221&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805222-trimmed.fastq ../fastq/SRR805222.fastq > reports_SRR805222&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805223-trimmed.fastq ../fastq/SRR805223.fastq > reports_SRR805223&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805224-trimmed.fastq ../fastq/SRR805224.fastq > reports_SRR805224&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805225-trimmed.fastq ../fastq/SRR805225.fastq > reports_SRR805225&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805226-trimmed.fastq ../fastq/SRR805226.fastq > reports_SRR805226&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805227-trimmed.fastq ../fastq/SRR805227.fastq > reports_SRR805227&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805228-trimmed.fastq ../fastq/SRR805228.fastq > reports_SRR805228&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805229-trimmed.fastq ../fastq/SRR805229.fastq > reports_SRR805229
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805230-trimmed.fastq ../fastq/SRR805230.fastq > reports_SRR805230&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805231-trimmed.fastq ../fastq/SRR805231.fastq > reports_SRR805231&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805232-trimmed.fastq ../fastq/SRR805232.fastq > reports_SRR805232&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805233-trimmed.fastq ../fastq/SRR805233.fastq > reports_SRR805233&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805234-trimmed.fastq ../fastq/SRR805234.fastq > reports_SRR805234&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805235-trimmed.fastq ../fastq/SRR805235.fastq > reports_SRR805235&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805236-trimmed.fastq ../fastq/SRR805236.fastq > reports_SRR805236&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805237-trimmed.fastq ../fastq/SRR805237.fastq > reports_SRR805237&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805238-trimmed.fastq ../fastq/SRR805238.fastq > reports_SRR805238&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805239-trimmed.fastq ../fastq/SRR805239.fastq > reports_SRR805239&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805240-trimmed.fastq ../fastq/SRR805240.fastq > reports_SRR805240&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805241-trimmed.fastq ../fastq/SRR805241.fastq > reports_SRR805241&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805242-trimmed.fastq ../fastq/SRR805242.fastq > reports_SRR805242&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805243-trimmed.fastq ../fastq/SRR805243.fastq > reports_SRR805243&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805244-trimmed.fastq ../fastq/SRR805244.fastq > reports_SRR805244&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805245-trimmed.fastq ../fastq/SRR805245.fastq > reports_SRR805245&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805246-trimmed.fastq ../fastq/SRR805246.fastq > reports_SRR805246&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805247-trimmed.fastq ../fastq/SRR805247.fastq > reports_SRR805247&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805248-trimmed.fastq ../fastq/SRR805248.fastq > reports_SRR805248&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805249-trimmed.fastq ../fastq/SRR805249.fastq > reports_SRR805249&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805250-trimmed.fastq ../fastq/SRR805250.fastq > reports_SRR805250&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805251-trimmed.fastq ../fastq/SRR805251.fastq > reports_SRR805251&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805252-trimmed.fastq ../fastq/SRR805252.fastq > reports_SRR805252&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805253-trimmed.fastq ../fastq/SRR805253.fastq > reports_SRR805253&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805254-trimmed.fastq ../fastq/SRR805254.fastq > reports_SRR805254&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805255-trimmed.fastq ../fastq/SRR805255.fastq > reports_SRR805255&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805256-trimmed.fastq ../fastq/SRR805256.fastq > reports_SRR805256&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805257-trimmed.fastq ../fastq/SRR805257.fastq > reports_SRR805257&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805258-trimmed.fastq ../fastq/SRR805258.fastq > reports_SRR805258&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805259-trimmed.fastq ../fastq/SRR805259.fastq > reports_SRR805259&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805260-trimmed.fastq ../fastq/SRR805260.fastq > reports_SRR805260&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805261-trimmed.fastq ../fastq/SRR805261.fastq > reports_SRR805261&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805262-trimmed.fastq ../fastq/SRR805262.fastq > reports_SRR805262&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805263-trimmed.fastq ../fastq/SRR805263.fastq > reports_SRR805263&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805264-trimmed.fastq ../fastq/SRR805264.fastq > reports_SRR805264&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805265-trimmed.fastq ../fastq/SRR805265.fastq > reports_SRR805265&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805266-trimmed.fastq ../fastq/SRR805266.fastq > reports_SRR805266&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805267-trimmed.fastq ../fastq/SRR805267.fastq > reports_SRR805267&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805268-trimmed.fastq ../fastq/SRR805268.fastq > reports_SRR805268&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805269-trimmed.fastq ../fastq/SRR805269.fastq > reports_SRR805269&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805270-trimmed.fastq ../fastq/SRR805270.fastq > reports_SRR805270&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805271-trimmed.fastq ../fastq/SRR805271.fastq > reports_SRR805271&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805272-trimmed.fastq ../fastq/SRR805272.fastq > reports_SRR805272&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805273-trimmed.fastq ../fastq/SRR805273.fastq > reports_SRR805273&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805274-trimmed.fastq ../fastq/SRR805274.fastq > reports_SRR805274&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805275-trimmed.fastq ../fastq/SRR805275.fastq > reports_SRR805275&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805276-trimmed.fastq ../fastq/SRR805276.fastq > reports_SRR805276&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805277-trimmed.fastq ../fastq/SRR805277.fastq > reports_SRR805277&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805278-trimmed.fastq ../fastq/SRR805278.fastq > reports_SRR805278&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805279-trimmed.fastq ../fastq/SRR805279.fastq > reports_SRR805279&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805280-trimmed.fastq ../fastq/SRR805280.fastq > reports_SRR805280&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805281-trimmed.fastq ../fastq/SRR805281.fastq > reports_SRR805281&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805282-trimmed.fastq ../fastq/SRR805282.fastq > reports_SRR805282&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805283-trimmed.fastq ../fastq/SRR805283.fastq > reports_SRR805283&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805284-trimmed.fastq ../fastq/SRR805284.fastq > reports_SRR805284&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805285-trimmed.fastq ../fastq/SRR805285.fastq > reports_SRR805285&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805286-trimmed.fastq ../fastq/SRR805286.fastq > reports_SRR805286&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805287-trimmed.fastq ../fastq/SRR805287.fastq > reports_SRR805287&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805288-trimmed.fastq ../fastq/SRR805288.fastq > reports_SRR805288&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805289-trimmed.fastq ../fastq/SRR805289.fastq > reports_SRR805289&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805173-trimmed.fastq ../fastq/SRR805173.fastq > reports_SRR805173&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805174-trimmed.fastq ../fastq/SRR805174.fastq > reports_SRR805174&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805175-trimmed.fastq ../fastq/SRR805175.fastq > reports_SRR805175&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805176-trimmed.fastq ../fastq/SRR805176.fastq > reports_SRR805176&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805177-trimmed.fastq ../fastq/SRR805177.fastq > reports_SRR805177&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805178-trimmed.fastq ../fastq/SRR805178.fastq > reports_SRR805178&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805179-trimmed.fastq ../fastq/SRR805179.fastq > reports_SRR805179&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805180-trimmed.fastq ../fastq/SRR805180.fastq > reports_SRR805180&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805181-trimmed.fastq ../fastq/SRR805181.fastq > reports_SRR805181&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805182-trimmed.fastq ../fastq/SRR805182.fastq > reports_SRR805182&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805183-trimmed.fastq ../fastq/SRR805183.fastq > reports_SRR805183&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805184-trimmed.fastq ../fastq/SRR805184.fastq > reports_SRR805184&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805185-trimmed.fastq ../fastq/SRR805185.fastq > reports_SRR805185&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805186-trimmed.fastq ../fastq/SRR805186.fastq > reports_SRR805186&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805187-trimmed.fastq ../fastq/SRR805187.fastq > reports_SRR805187&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805188-trimmed.fastq ../fastq/SRR805188.fastq > reports_SRR805188&
/home/gex/work/RNAseq/cutadapt-1.4.1/bin/cutadapt  -a AAGCAGTGGTATCAACGCAGAGTACATGGG   -a AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -e 0.1 -O 5 -m 15 --quality-base=64 -q 15 -o SRR805189-trimmed.fastq ../fastq/SRR805189.fastq > reports_SRR805189&

##########################################################
# 3. Using Tophat to map read to genomes
# This is a Perl script to generate PBS scripts for running
# on PC cluster. This script may have issues as it may not be the most up to date version. 
##########################################################
	#!/usr/bin/env perl
	#234567890123456789012345678901234567890123456789012345678901234567890123456789
	use warnings;
	use strict;
	
	# Perl script: bowtie_runs2
	system("rm *.pbs*");
	open (my $fh, "files.list.txt") or die "Could not fine file!";
	
	my @files = <$fh>;
	
	foreach my $file (@files) {
	            chomp $file;
	            my $base = $file;
	
	    my $outfile = $base.".pbs";
	    print "$outfile ";
	#    print "Output file name is $outfile \n";
	    open OUTPUT,">$outfile";
	
	    print OUTPUT "#!/bin/bash\n";
	    print OUTPUT "\n";
	    print OUTPUT "#PBS -q batch2\n";
	    print OUTPUT "#PBS -l nodes=1:ppn=12\n";
	    print OUTPUT "#PBS -l walltime=26:00:00\n";
	    print OUTPUT "#PBS -W x=NACCESSPOLICY:SINGLEJOB\n";
	    print OUTPUT "\n";
	    print OUTPUT "cd \$PBS_O_WORKDIR \n";
	    print OUTPUT ". /usr/share/modules/init/sh\n";
	    print OUTPUT "module load bio/bowtie2/2.2.4\n";
	    print OUTPUT "module load bio/tophat/2.0.13\n";
	    print OUTPUT "\n";
	    print OUTPUT "date\n";
	    print OUTPUT "tophat2 -p 12  -N   3  --no-coverage-search  --solexa1.3-quals  --b2-very-sensitive   --read-edit-dist 3  --transcriptome-index=transcriptome_data/ensembl genome ".$base."_trimmed.fastq\n";
	    print OUTPUT "date\n";
	
	    close OUTPUT;
	    #exit;
	     system("qsub",$outfile);
	
	}
	print "\n";

##########################################################
# 4. Using Cufflinks to assemble transcriptomes
# This is a Perl script to generate PBS scripts for running
# on PC cluster
##########################################################	


	use warnings;
	use strict;
	system("rm *.pbs*");
	my @files = <SRR*_accepted_hits.bam>;
	
	foreach my $file (@files) {
	    my ($base,$ext) = split "_",$file;
	    my $infile_name = $file;
	    my $outfile = $base.".pbs";
	    print "$outfile ";
	    open OUTPUT,">$outfile";
	    print OUTPUT "#!/bin/bash\n";
	    print OUTPUT "\n";
	    print OUTPUT "#PBS -q batch2\n";
	    print OUTPUT "#PBS -l nodes=1:ppn=12\n";
	    print OUTPUT "#PBS -l walltime=26:00:00\n";
	    print OUTPUT "#PBS -W x=NACCESSPOLICY:SINGLEJOB\n";
	    print OUTPUT "\n";
	    print OUTPUT "cd \$PBS_O_WORKDIR \n";
	    print OUTPUT ". /usr/share/modules/init/sh\n";
	    print OUTPUT "module load bio/cufflinks/2.2.1\n";
	    print OUTPUT "\n";
	    print OUTPUT "date\n";
	    print OUTPUT "cufflinks -p 12  -b genome.fa -u -o ".$base."_clout  -g genes.gtf  $file 2>report_$base\n";
	    print OUTPUT "date\n";
	
	    close OUTPUT;
	    #exit;
	    system("qsub",$outfile);
	
	}
	print "\n";
	
##########################################################
# 5.  Cuffmerge 
# this is Linux Shell script
##########################################################	

	cuffmerge -g genes.gtf  -s genome.fa -p 50 assemblies.txt
	
	Where assemblies.txt contains the names of cufflink results
	./SRR805430_clout/transcripts.gtf
	./SRR805431_clout/transcripts.gtf
	./SRR805432_clout/transcripts.gtf
	./SRR805433_clout/transcripts.gtf
	./SRR805434_clout/transcripts.gtf
	./SRR805435_clout/transcripts.gtf
	./SRR805436_clout/transcripts.gtf
	./SRR805437_clout/transcripts.gtf
	
	This generates a merged.gtf file
##########################################################
# 6.  Cuffquant 
# This is a Perl script to generate PBS scripts for running
# on PC cluster
##########################################################	

	#!/usr/bin/env perl
	#234567890123456789012345678901234567890123456789012345678901234567890123456789
	use warnings;
	use strict;
	
	# Perl script: bowtie_runs2
	system("rm *.pbs*");
	my @files = <SRR*_accepted_hits.bam>;
	
	foreach my $file (@files) {
	    my ($base,$ext) = split "_",$file;
	    my $infile_name = $file;
	    my $outfile = "cuffquant".$base.".pbs";
	    print "$outfile ";
	#    print "Output file name is $outfile \n";
	    open OUTPUT,">$outfile";
	
	    print OUTPUT "#!/bin/bash\n";
	    print OUTPUT "\n";
	    print OUTPUT "#PBS -q batch2\n";
	    print OUTPUT "#PBS -l nodes=1:ppn=12\n";
	    print OUTPUT "#PBS -l walltime=26:00:00\n";
	    #print OUTPUT "#PBS -W x=NACCESSPOLICY:SINGLEJOB\n";
	    print OUTPUT "\n";
	    print OUTPUT "cd \$PBS_O_WORKDIR \n";
	    print OUTPUT ". /usr/share/modules/init/sh\n";
	    print OUTPUT "module load bio/cufflinks/2.2.1\n";
	    print OUTPUT "\n";
	    print OUTPUT "date\n";
	    print OUTPUT "cuffquant -p 12  -b genome.fa -u -o ".$base."  merged.gtf  $file 2>report_$base\n";
	    print OUTPUT "date\n";
	
	    close OUTPUT;
	    system("qsub",$outfile);
	
	}
	print "\n";

#########################################################
### 7.  Cuffnorm
# Linux script; 	Cuffnorm  needs large memory.
#########################################################
	
	cuffnorm -o cuffnorm -p 30 merged.gtf  \
	abundances/abundances/SRR1041764_abundances.cxb \
	abundances/abundances/SRR1041763_abundances.cxb \
	abundances/abundances/SRR1041762_abundances.cxb \
	abundances/abundances/SRR1041761_abundances.cxb \
	abundances/abundances/SRR1041760_abundances.cxb \
	abundances/abundances/SRR1041759_abundances.cxb

#########################################################
8. Create genome index for STAR
#########################################################
./STAR --runThreadN 10 --runMode genomeGenerate --genomeDir mm10_index  --sjdbGTFfile  /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --genomeFastaFiles  /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa  --sjdbOverhang  51
#########################################################
9. Genome Mapping using STAR
#########################################################
for FILES in  ../../mouse/trimmed/*.gz
do
FQ=`echo $FILES | sed 's/-trimmed.fastq.gz//' | sed 's/.*SRR/SRR/'`
echo $FQ
../STAR --runThreadN  10  --genomeDir ../mm10_index   --readFilesIn  $FILES  --readFilesCommand zcat --outFilterMultimapNmax 100  --winAnchorMultimapNmax 100 --outSAMmultNmax 100  --outSAMtype BAM SortedByCoordinate   --outFilterMismatchNmax 3
mv Aligned.sortedByCoord.out.bam ${FQ}.STAR.bam
mv  Log.final.out ${FQ}.STAR.Log.final.out
done


#########################################################
10. Retrotransposon expression using TEtranscripts
#########################################################

TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples1  -t  SRR1041728.STAR.bam SRR1041729.STAR.bam SRR1041730.STAR.bam SRR1041731.STAR.bam SRR1041732.STAR.bam  -c  SRR1041733.STAR.bam SRR1041734.STAR.bam SRR1041735.STAR.bam SRR1041736.STAR.bam SRR1041737.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples11  -t  SRR1041738.STAR.bam SRR1041739.STAR.bam SRR1041740.STAR.bam SRR1041741.STAR.bam SRR1041742.STAR.bam  -c  SRR1041743.STAR.bam SRR1041744.STAR.bam SRR1041745.STAR.bam SRR1041746.STAR.bam SRR1041747.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples21  -t  SRR1041748.STAR.bam SRR1041749.STAR.bam SRR1041750.STAR.bam SRR1041751.STAR.bam SRR1041752.STAR.bam  -c  SRR1041753.STAR.bam SRR1041754.STAR.bam SRR1041755.STAR.bam SRR1041756.STAR.bam SRR1041757.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples31  -t  SRR1041758.STAR.bam SRR1041759.STAR.bam SRR1041760.STAR.bam SRR1041761.STAR.bam SRR1041762.STAR.bam  -c  SRR1041763.STAR.bam SRR1041764.STAR.bam SRR805173.STAR.bam SRR805174.STAR.bam SRR805175.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples41  -t  SRR805176.STAR.bam SRR805177.STAR.bam SRR805178.STAR.bam SRR805179.STAR.bam SRR805180.STAR.bam  -c  SRR805181.STAR.bam SRR805182.STAR.bam SRR805183.STAR.bam SRR805184.STAR.bam SRR805185.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples51  -t  SRR805186.STAR.bam SRR805187.STAR.bam SRR805188.STAR.bam SRR805189.STAR.bam SRR805190.STAR.bam  -c  SRR805191.STAR.bam SRR805192.STAR.bam SRR805193.STAR.bam SRR805194.STAR.bam SRR805195.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples61  -t  SRR805196.STAR.bam SRR805197.STAR.bam SRR805198.STAR.bam SRR805199.STAR.bam SRR805200.STAR.bam  -c  SRR805201.STAR.bam SRR805202.STAR.bam SRR805203.STAR.bam SRR805204.STAR.bam SRR805205.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples71  -t  SRR805206.STAR.bam SRR805207.STAR.bam SRR805208.STAR.bam SRR805209.STAR.bam SRR805210.STAR.bam  -c  SRR805211.STAR.bam SRR805212.STAR.bam SRR805213.STAR.bam SRR805214.STAR.bam SRR805215.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples81  -t  SRR805216.STAR.bam SRR805217.STAR.bam SRR805218.STAR.bam SRR805219.STAR.bam SRR805220.STAR.bam  -c  SRR805221.STAR.bam SRR805222.STAR.bam SRR805223.STAR.bam SRR805224.STAR.bam SRR805225.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples91  -t  SRR805226.STAR.bam SRR805227.STAR.bam SRR805228.STAR.bam SRR805229.STAR.bam SRR805230.STAR.bam  -c  SRR805231.STAR.bam SRR805232.STAR.bam SRR805233.STAR.bam SRR805234.STAR.bam SRR805235.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples101  -t  SRR805236.STAR.bam SRR805237.STAR.bam SRR805238.STAR.bam SRR805239.STAR.bam SRR805240.STAR.bam  -c  SRR805241.STAR.bam SRR805242.STAR.bam SRR805243.STAR.bam SRR805244.STAR.bam SRR805245.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples111  -t  SRR805246.STAR.bam SRR805247.STAR.bam SRR805248.STAR.bam SRR805249.STAR.bam SRR805250.STAR.bam  -c  SRR805251.STAR.bam SRR805252.STAR.bam SRR805253.STAR.bam SRR805254.STAR.bam SRR805255.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples121  -t  SRR805256.STAR.bam SRR805257.STAR.bam SRR805258.STAR.bam SRR805259.STAR.bam SRR805260.STAR.bam  -c  SRR805261.STAR.bam SRR805262.STAR.bam SRR805263.STAR.bam SRR805264.STAR.bam SRR805265.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples131  -t  SRR805266.STAR.bam SRR805267.STAR.bam SRR805268.STAR.bam SRR805269.STAR.bam SRR805270.STAR.bam  -c  SRR805271.STAR.bam SRR805272.STAR.bam SRR805273.STAR.bam SRR805274.STAR.bam SRR805275.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples141  -t  SRR805276.STAR.bam SRR805277.STAR.bam SRR805278.STAR.bam SRR805279.STAR.bam SRR805280.STAR.bam  -c  SRR805281.STAR.bam SRR805282.STAR.bam SRR805283.STAR.bam SRR805284.STAR.bam SRR805285.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples151  -t  SRR805286.STAR.bam SRR805287.STAR.bam SRR805288.STAR.bam SRR805289.STAR.bam SRR805290.STAR.bam  -c  SRR805291.STAR.bam SRR805292.STAR.bam SRR805293.STAR.bam SRR805294.STAR.bam SRR805295.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples161  -t  SRR805296.STAR.bam SRR805297.STAR.bam SRR805298.STAR.bam SRR805299.STAR.bam SRR805300.STAR.bam  -c  SRR805301.STAR.bam SRR805302.STAR.bam SRR805303.STAR.bam SRR805304.STAR.bam SRR805305.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples171  -t  SRR805306.STAR.bam SRR805307.STAR.bam SRR805308.STAR.bam SRR805309.STAR.bam SRR805310.STAR.bam  -c  SRR805311.STAR.bam SRR805312.STAR.bam SRR805313.STAR.bam SRR805314.STAR.bam SRR805315.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples181  -t  SRR805316.STAR.bam SRR805317.STAR.bam SRR805318.STAR.bam SRR805319.STAR.bam SRR805320.STAR.bam  -c  SRR805321.STAR.bam SRR805322.STAR.bam SRR805323.STAR.bam SRR805324.STAR.bam SRR805325.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples191  -t  SRR805326.STAR.bam SRR805327.STAR.bam SRR805328.STAR.bam SRR805329.STAR.bam SRR805330.STAR.bam  -c  SRR805331.STAR.bam SRR805332.STAR.bam SRR805333.STAR.bam SRR805334.STAR.bam SRR805335.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples201  -t  SRR805336.STAR.bam SRR805337.STAR.bam SRR805338.STAR.bam SRR805339.STAR.bam SRR805340.STAR.bam  -c  SRR805341.STAR.bam SRR805342.STAR.bam SRR805343.STAR.bam SRR805344.STAR.bam SRR805345.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples211  -t  SRR805346.STAR.bam SRR805347.STAR.bam SRR805348.STAR.bam SRR805349.STAR.bam SRR805350.STAR.bam  -c  SRR805351.STAR.bam SRR805352.STAR.bam SRR805353.STAR.bam SRR805354.STAR.bam SRR805355.STAR.bam &

TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples201b  -t  SRR805336.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples202  -t  SRR805337.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples203  -t  SRR805338.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples204  -t  SRR805339.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples205  -t  SRR805340.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples206  -t  SRR805341.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples207  -t  SRR805342.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples208  -t  SRR805343.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples209  -t  SRR805344.STAR.bam  -c SRR805429.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples210  -t  SRR805345.STAR.bam  -c SRR805429.STAR.bam &

TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples221  -t  SRR805356.STAR.bam SRR805357.STAR.bam SRR805358.STAR.bam SRR805359.STAR.bam SRR805360.STAR.bam  -c  SRR805361.STAR.bam SRR805362.STAR.bam SRR805363.STAR.bam SRR805364.STAR.bam SRR805365.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples231  -t  SRR805366.STAR.bam SRR805367.STAR.bam SRR805368.STAR.bam SRR805369.STAR.bam SRR805370.STAR.bam  -c  SRR805371.STAR.bam SRR805372.STAR.bam SRR805373.STAR.bam SRR805374.STAR.bam SRR805375.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples241  -t  SRR805376.STAR.bam SRR805377.STAR.bam SRR805378.STAR.bam SRR805379.STAR.bam SRR805380.STAR.bam  -c  SRR805381.STAR.bam SRR805382.STAR.bam SRR805383.STAR.bam SRR805384.STAR.bam SRR805385.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples251  -t  SRR805386.STAR.bam SRR805387.STAR.bam SRR805388.STAR.bam SRR805389.STAR.bam SRR805390.STAR.bam  -c  SRR805391.STAR.bam SRR805392.STAR.bam SRR805393.STAR.bam SRR805394.STAR.bam SRR805395.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples261  -t  SRR805396.STAR.bam SRR805397.STAR.bam SRR805398.STAR.bam SRR805399.STAR.bam SRR805400.STAR.bam  -c  SRR805401.STAR.bam SRR805402.STAR.bam SRR805403.STAR.bam SRR805404.STAR.bam SRR805405.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples271  -t  SRR805406.STAR.bam SRR805407.STAR.bam SRR805408.STAR.bam SRR805409.STAR.bam SRR805410.STAR.bam  -c  SRR805411.STAR.bam SRR805412.STAR.bam SRR805413.STAR.bam SRR805414.STAR.bam SRR805415.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples281  -t  SRR805416.STAR.bam SRR805417.STAR.bam SRR805418.STAR.bam SRR805419.STAR.bam SRR805420.STAR.bam  -c  SRR805421.STAR.bam SRR805422.STAR.bam SRR805423.STAR.bam SRR805424.STAR.bam SRR805425.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples291  -t  SRR805426.STAR.bam SRR805427.STAR.bam SRR805428.STAR.bam SRR805429.STAR.bam SRR805430.STAR.bam  -c  SRR805431.STAR.bam SRR805432.STAR.bam SRR805433.STAR.bam SRR805434.STAR.bam SRR805435.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples301  -t  SRR805436.STAR.bam SRR805437.STAR.bam SRR805438.STAR.bam SRR805439.STAR.bam SRR805440.STAR.bam  -c  SRR805441.STAR.bam SRR805442.STAR.bam SRR805443.STAR.bam SRR805444.STAR.bam SRR805445.STAR.bam &
TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples311  -t  SRR805446.STAR.bam SRR805447.STAR.bam SRR805448.STAR.bam SRR805449.STAR.bam SRR805450.STAR.bam  -c  SRR805451.STAR.bam SRR805452.STAR.bam    &

TEtranscripts --format BAM --mode multi  --GTF /home/gex/work/RNAseq/STAR/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --TE ../mm10_rmsk_TE.gtf  -i 2 --stranded no  --project samples311  -t  SRR805446.STAR.bam SRR805447.STAR.bam SRR805448.STAR.bam SRR805449.STAR.bam SRR805450.STAR.bam  -c  SRR805451.STAR.bam SRR805452.STAR.bam    &