DESeq2 giving 0 output lines

Hello! I am fairly new to Galaxy, and am trying to complete a differential gene expression analysis. The tools I am using are HISAT2, featureCounts, and then DESeq2. I have run all of the programs successfully until DESeq2. DESeq2 will run and complete successfully (turns green), but it gives me 0 lines for the output, so I don’t actually receive any results. Why is this happening?

Any help is appreciated! Thanks in advance!

Hi @edenbishop

Please try at least one rerun first.

If that also fails, double checking the inputs is the next step. This forum has much Q&A about what has worked for others, and the GTN tutorials have examples. If you get stuck, please consider posting back a shared history link and we can take a closer look. Troubleshooting errors

Hi @jennaj ,

Thanks for the reply! I did a rerun and got an error that time. My issue was that I was using different featureCount files with the same name. I have started over and DESeq2 runs successfully now and actually gives output lines, so I’m all good!
Thanks for the help!

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