how to run deseq2 on a sample .tsv file

I am trying to run the deseq2 method on a tsv file I downloaded from ebi. the file has all the data, but galaxy history somehow turns red and doesn’t finish the job. is there any preprocessing that I am not doing or maybe I need a different format than tsv? please help.

Hi @Arsalan_Maleki

What is the assigned datatype? tvs (tab separated values) files have the datatype tabular in Galaxy. It is usually best to let Galaxy auto-detect the datatype during Upload, but if you already directly assigned a datatype instead, try to re-detect to see what results: faqs/galaxy/#detecting-the-datatype-file-format. If Galaxy doesn’t guess tabular then there is likely a format problem.

DESeq2 will expect multiple inputs. These tutorials cover usage examples: search?query=deseq2

This forum also has much Q&A around troubleshooting inputs for this tool and related tools. Try searching this forum with keywords like the tool name or datatype. I also added some tags that will do the same.

If you need more help or get stuck, please explain a bit more about how you are using the tool. Creating and posting back a shared history link would be helpful. faqs/galaxy/#sharing-your-history. Please leave all input and output datasets undeleted for the best feedback.