18 Mar
2011
18 Mar
'11
9:34 a.m.
It looks like the output only occurs when cufflinks can't run on the provided dataset. I checked my inputs, and I think that is the problem...its a sam file from bowtie, not from tophat, hence not a sorted sam file. Perhaps this stderr message doesn't matter after all, its just misleading...
Yes, I think you are correct. Let us know if you have more questions. Best, J.