Trim-Align-Count-One-Condition-Paired

Annotation:

StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: FastQC
Output dataset 'output' from step 1
select at runtime
select at runtime
Step 3: Trimmomatic
Paired-end (as collection)
Output dataset 'output' from step 1
False
Trimmomatic Operations
Trimmomatic Operation 1
Sliding window trimming (SLIDINGWINDOW)
4
20
Use default job resource parameters
Step 4: HISAT2
FASTQ
Paired reads
Individual files
Output dataset 'fastq_out_r1_paired' from step 3
Output dataset 'fastq_out_r2_paired' from step 3
Use default values
False
False
Use a built-in genome
Not available.
Not available.
Not available.
False
Use default values
Use default values
Use default values
Use default values
Use default values
Use default job resource parameters
Step 5: StringTie
Output dataset 'output_alignments' from step 4
Do not use GFF/GTF
Use defaults
Use default job resource parameters
Step 6: htseq-count
Output dataset 'output_alignments' from step 4
Output dataset 'coverage' from step 5
Union
Yes
10
exon
gene_id
Do not output additional BAM file
False