RNAseq_pairedend_pairedcollection

Annotation:

StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Trim Galore!
Paired Collection
Output dataset 'output' from step 1
Automatic detection
False
Not available.
Not available.
Use defaults
Use defaults (no RRBS)
Remove illumina adapter sequences.
Step 5: FastQC
Output dataset 'trimmed_reads_paired_collection' from step 4
select at runtime
select at runtime
Step 6: HISAT2
Use a genome from history
Output dataset 'output' from step 2
Paired-end Dataset Collection
Output dataset 'trimmed_reads_paired_collection' from step 4
Unstranded
Use default values
Summary Options:
False
False
Advanced Options:
Use default values
Use default values
Use default values
Use default values
Use default values
Use default values
Use default values
Use default job resource parameters
Step 7: featureCounts
Output dataset 'output_alignments' from step 6
Unstranded
in your history
Output dataset 'output' from step 3
Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)
False
Options for paired-end reads:
Disabled; all reads/mates will be counted individually
False
True
Advanced options:
gene
ID
False
False
Disabled; multi-mapping reads are excluded (default)
12
False
False
False
False
1
0
0
0
0
Leave the read as it is
False
False
False
False
GFF gene identifer changed to 'ID' from 'geneID' because of the formatting of the particular .bam files. Check ninth column of the bam files for which identifier is being used.