CuffDiff maximum number of sam/bam files

[Mtakai]

Hi all,
Currently using cuffdiff to look a RNAseq from 31 samples. When I use the samples, the program stalls at 2% hence is there a limit to the number of bam files that can be provided? It works when I provide only two.

Thanks in advance.

Mtakai

[peromhc]

Does it work when you provide only a couple of files from each treatment/condition? How long have you let it sit at 2%-- it is just 'thinking'

[Mtakai]

Yeah, did work when I provided only a couple of file from each treatment and left it to sit for about 4hrs. Seems to be working now with the 31 files, I guess cuffdiff just needs more time.

Thanks for the response peromhc.