Hello, I am trying to learn how to process RNA-Seq datasets with Galaxy to compute read counts per gene.
As far as I understand, I need to get a file with the reads, and then map it to a genome, then pass the map to featureCounts to get the actual counts.
Therefore, I created a workflow that is supposed to go from reads to counts.
I started with the NCBI SRA Tools -> Extract reads tool, and I used SRR1975453 as SRR accession, as a test.
Next, I put the Bowtie2 tool, using the output_file of the first tool as the input FASTQ file
Last, I used featureCounts, with the BAM that comes out of Bowtie2 as input.
This is the workflow: https://usegalaxy.org/u/mdonato/w/test-rnaseq
My issue is that when I run that workflow, only the first step runs, and then it stops without giving me any error.
Does anybody have any idea why that doesn't work?