Question: Workflow only runs first step and then stops
gravatar for mdonato
21 months ago by
mdonato0 wrote:

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:

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?

rna-seq • 536 views
ADD COMMENTlink written 21 months ago by mdonato0
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