Hi, First of all sorry for posting about cufflinks here... 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 -- Sent via the guest posting facility at bioconductor.org.

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 Best, Jim > > 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099