Concatenate mutiple samples from tophat to run cuffdiff

Question

[bigjay2578]

I have run tophat one multiple files. I have 16 samples total, four in each of four different conditions. I would like to run cuffdiff one say the four of one condition vs the four of another condition. Cuffdiff doesn't seem to accept more than two accepted hits files at the command line (or I'm just not doing it right). Is there a way to run eight files at once under two condtions using cuffdiff?

Answer 1

[seidel]

From the cuffdiff manual:

If you have more than one replicate for a sample, supply the SAM files for the sample as a single comma-separated list. It is not necessary to have the same number of replicates for each sample.

Note that Cuffdiff can also accepted BAM files...

Are you specifying each set of replicates as a comma-separated list?