Question: Cuffdiff - Doesn'T Appear To Be A Valid Bam File
gravatar for mllmmllmmllmm
7.7 years ago by
mllmmllmmllmm0 wrote:


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


cuffdiff • 2.9k views
ADD COMMENTlink written 7.7 years ago by mllmmllmmllmm0
gravatar for Ryan Thompson
7.7 years ago by
Ryan Thompson3.4k
TSRI, La Jolla, CA
Ryan Thompson3.4k wrote:

You could try doing a null conversion from bam to bam with samtools:

samtools view -h repA2.bam | samtools -bS -o repA2-new.bam -
mv repA2.bam repA2-old.bam
mv repA2-new.bam repA2.bam

In theory this should result in an identical file, but maybe it will smooth out whatever anomaly is tripping up cuffdiff. But I'm surprised that cufflinks accepts the file but cuffdiff doesn't. I believe they use the same code for reading BAM files. Mayeb you should double-check that your cufflinks and cuffdiff commands are from the same version of the Cufflinks distribution.

ADD COMMENTlink written 7.7 years ago by Ryan Thompson3.4k
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