I am struggling with the final steps of my RNA-Seq pipeline. The data has been cleaned up, mapped using HISAT2, transcriptomes created using both stringtie and cufflinks (to see if one or the other would solve the cummeRbund problem) then merged and cuffdiff was run. My cuffdiff tables show some significant changes in transcripts between two conditions, but when I attempt to run cummeRbund on the sqlite file, it cannot recognize the Gene_ID column. There is no dropdown menu to select transcripts, it just says "null".
The samples I'm using come from the http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html
I assumed the problem was on my end, I had not processed something correctly, so I went digging into the wrapper github website and found their test .sqlite file. https://github.com/galaxyproject/tools-devteam/blob/master/tools/cummerbund/test-data/cuffdiff_out.sqlite I loaded it into galaxy and tried to run cummeRbund on it, but it still does not give me options to select Genes under Gene_ID, it still says null.
If I had an sqlite file that worked with galaxy cummerbund, then I could start looking at my sqlite file and try to understand how it is different. If anyone has successfully done this, I would love to see your sqlite file!
I'm preparing an RNA-Seq workshop for a course and wanted to keep the entire thing in galaxy rather than trying to teach R in the last few hours of the workshop. However, I would really like the students to be able to generate some figures at the end of the analysis.
Thank you, Courtney