I am trying to run Cuffdiff, but it doesn't seem to be working. When I run the script, the following message comes up:
You are using Cufflinks v2.2.1, which is the most recent release.
And then it stops running and produces empty output files.
Why is this happening?
I tried sorting the SAM files a few different ways, but that doesn't seem to help. What SAMtools command should I be using to convert and sort the files (I used HiSat2 for alignment)?
Also, do I need to use Cufflinks to assemble the transcriptome? A file in the correct format was included in the reference genome download.
Thank you. Please respond ASAP.