| Step | Annotation |
|---|---|
|
Step 1: Input dataset
select at runtime
|
GRCh37_canon.fa (Ensembl reference fasta with only chromosome assigned sequences) |
|
Step 2: Input dataset
select at runtime
|
Homo_sapiens.GRCh37_canon.73.gtf |
|
Step 3: Input dataset
select at runtime
|
Homo_sapiens.GRCh37.73.pep.all.fa |
|
Step 4: Input dataset
select at runtime
|
RNA-Seq left mate pair fastq (These should be in fastqsanger format. If not, convert with "Fastq Groomer" tool.) |
|
Step 5: Input dataset
select at runtime
|
RNA-Seq right mate pair fastq (These should be in fastqsanger format. If not, convert with "Fastq Groomer" tool.) |
|
Step 6: RSEM prepare reference
reference genome and gtf
Output dataset 'output' from step 1
Output dataset 'output' from step 2
select at runtime
primaryEnsemblGtfRef
Add poly(A) tails to all transcripts
125
False
|
Given a GTF file and the reference genome, this tool constructs a synthetic transcriptome that will be used for isoform quantification during "-calculate expression". |
|
Step 7: FASTA-to-Tabular
Output dataset 'output' from step 3
1
0
|
|
|
Step 8: RSEM calculate expression
rsem_sample
From your history
Output dataset 'reference_file' from step 6
FASTQ
phred33 qualities (default for sanger)
Paired End Reads
Output dataset 'output' from step 4
Output dataset 'output' from step 5
use bowtie defaults
25
No
Use RSEM Defaults
No BAM results files
|
Given then RNA-Seq reads (fastq) and synthetic transcriptome (from "-prepare reference"), this tool quantifies the abundances of each mRNA transcript within the GTF file. |
|
Step 9: Cut
c1
Tab
Output dataset 'output' from step 7
|
|
|
Step 10: Filter
Output dataset 'isoform_abundances' from step 8
c3>0.000001
0
|
Selection of lower threshold of transcriptional abundance in TPM required for inclusion of the corresponding protein in the reduced database. |
|
Step 11: Convert
Whitespaces
Output dataset 'out_file1' from step 9
|
|
|
Step 12: Compute
c3*1000000
Output dataset 'out_file1' from step 10
NO
|
|
|
Step 13: Cut
c5
Tab
Output dataset 'out_file1' from step 11
|
|
|
Step 14: Convert
Colons
Output dataset 'out_file1' from step 13
|
|
|
Step 15: Cut
c2
Tab
Output dataset 'out_file1' from step 14
|
|
|
Step 16: Paste
Output dataset 'output' from step 7
Output dataset 'out_file1' from step 15
Tab
|
|
|
Step 17: Join two Datasets
Output dataset 'out_file1' from step 16
3
(value not yet validated)
Output dataset 'out_file1' from step 12
1
(value not yet validated)
No
No
No
|
|
|
Step 18: Add column
Output dataset 'out_file1' from step 17
NO
|
|
|
Step 19: Add column
tpm:
Output dataset 'out_file1' from step 18
NO
|
|
|
Step 20: Merge Columns
Output dataset 'out_file1' from step 19
1
(value not yet validated)
9
(value not yet validated)
Columns
Columns 1
10
(value not yet validated)
Columns 2
8
(value not yet validated)
|
|
|
Step 21: Cut
c11,c2
Tab
Output dataset 'out_file1' from step 20
|
|
|
Step 22: Tabular-to-FASTA
Output dataset 'out_file1' from step 21
1
(value not yet validated)
2
(value not yet validated)
|
Final reduced database after application of a TPM cut-off. |
|
Step 23: FASTA Width
Output dataset 'output' from step 22
80
|
Format FASTA to desired width. |