This is what I get when trying to run cuffdiff (cufflinks 2.0) with bam from tophat 1.4.1 using command is for diff analysis without trans. discovery
'repA2.bam doesn't appear to be a valid BAM file'
cuffdiff genes.gtf rep1.bam,rep2.bam \ repA2.bam,repA2.bam
btw, cufflinks takes the file without problems
thanks in advance