Additional File 3.txt: Commands used to process raw fastq files.

##Commands used to process raw fastq files:

#trim adapters:
seqtk trimfq {input_file}  > {output_file}.seqtk.fq

#filter and trim low quality reads
java -jar trimmomatic-0.39.jar SE -phred33 {output_file}.seqtk.fq {output_file}_filtered -threads 5 AVGQUAL:20 MINLEN:20

#To map with STAR:

STAR --runThreadN 10 --genomeDir {genome} --readFilesIn {input_file} --readFilesCommand gunzip -c --outFileNamePrefix {output_file} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --chimOutType Junctions --twopassMode Basic --twopass1readsN -1  --quantMode TranscriptomeSAM GeneCounts

#To count expression with Kallisto:
kallisto quant -i {genome} -o {output_file} --single --fusion --bias -t 12 -b 10 -l 150 -s 70 --rf-stranded -g {gtf} {input_file}