SRR to counts

Annotation:

StepAnnotation
Step 1: Download and Extract Reads in FASTA/Q
SRR accession
SRR1975453
Uncompressed fastq
Advanced Options:
Not available.
Not available.
Not available.
True
both
Empty.
Empty.
None
Empty.
False
False
Empty.
Step 2: Bowtie2
Single-end
Output dataset 'output_file' from step 1
False
False
Use a built-in genome index
hg38
Do not set
1: Default setting only
Very fast end-to-end (--very-fast)
False
Use default job resource parameters
Step 3: featureCounts
Output dataset 'output' from step 2
locally cached
hg38.gtf
Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)
False
Options for paired-end reads:
Disabled; all reads/mates will be counted individually
False
Forward, Reverse (fr)
True
Advanced options:
exon
gene_id
False
False
Unstranded
Disabled; multi-mapping reads are excluded (default)
12
False
1
0
0
Leave the read as it is
False
False
False
Use default job resource parameters