cuffdiff software output

Hello. I am using cuffdiff in the galaxy. Between my cuffdiff output, there are no isoforms differential expression file and I get 17 files in my output instead of 23. how can I get isoforms differential expression file?
please guide me.
thank you.

Hi @Sevda.Hosseinzadeh

Updated transcriptomic analysis methods are strongly recommended, and many tools for transcriptomics analysis are covered in the Galaxy tutorials here: Galaxy Training!. You can also review the RNA-seq or RNA Analysis tool groups.

If you get stuck with a non-deprecated tool, review this troubleshooting FAQ first, then ask questions here with the context from your troubleshooting and a shared history.

Cuffdiff and many other of the “Cuff” tools are deprecated on most public Galaxy servers. Check to see if this, or any of the tools that you may have used upstream, is marked deprecated where you are working. Deprecated tools may directly fail, or they might just produce odd results.

Even if the “Cuff” tool is not marked as deprecated on a particular server, it may still produce odd results or have limited/modified results for technical reasons. These tools won’t be updated. That said, common problems that people used to run into usually involved the reference annotation. Upstream from that, the BAM sometimes had problems. Both were usually about missing attributes or format issues.

This link points to a search of our prior forum with the keywords “biostars cuffdiff”. That may not fix the problem you are having (missing expected outputs), but if you really want to use the old tool, checking the usage/inputs for prior known issues is where to start.

To do your own search, go to the Pan-Galactic Google Search and add in the search term (names other “Cuff” tools used upstream? or the mapping tool?) along with the keyword “biostars” to limit the results. This forum doesn’t include that original discussion since it started being used a few years after those tools were deprecated.

Thank you very much.