[BioC] doesn\'t appear to be a valid BAM file

James W. MacDonald jmacdon at uw.edu
Tue Oct 16 19:43:14 CEST 2012

Hi Michael,

On 10/16/2012 1:36 PM, Michael [guest] wrote:
> Hi,
> First of all sorry for posting about cufflinks here...

As you already know, this isn't the right list. On the cufflinks website 
there is this:

    _Getting Help_

Questions about Cufflinks should be sent to *tophat.cufflinks at gmail.com* 
<mailto:tophat.cufflinks at gmail.com>. Please do not email technical 
questions to Cufflinks contributors directly.

Which is probably your best bet. Alternatively you could try seqanswers.com



> 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
> thanks in advance :)
>   -- output of sessionInfo():
> x
> --
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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