Cuffdiff - 'the file doesn't appear to be a valid BAM file

[ekimmike]

Hi,

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

Michael

[masterpiece]

cuffdiff genes.gtf rep1.bam,rep2.bam \ repA2.bam,repA2.bam

Did you run cuffdiff with '\' in the command? Remove the '\', leave a space between the 2 samples and run the command

[ekimmike]

Thanks! now it works

btw, do you have any idea why it takes so long to run cuffdiff on bam files without transcript discovery
bam files were generated supporting tophat with gene models from genes.gtf

here is my command:
cuffdiff -o cuffdiff -b genome.fa -u genes.gtf -L A,B,C,D bam files (2 replicates)


is <-b genome.fa> the reason?