Question: Cuffdiff problems as part of a tutorial
gravatar for k.l.noel
3 months ago by
k.l.noel0 wrote:


I have a problem with Cuffdiff, having successfully executed Tophat, Cufflink and Cuffmerge on RNAseq data as part of a tutorial. Here is the error message I received.

Fatal error: Exit code 1 () Error: sort order of reads in BAMs must be the same

I tried to run Cuffdiff twice and it did not work.

Any suggestions would be appreciated.



rna-seq gtf genome sort cuffdiff • 129 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson24k • written 3 months ago by k.l.noel0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson24k wrote:


The error is coming up because some of the Tophat jobs were mapped against papHam1 (the default in the target database/genome select list on the tool form) instead of actively selected to be hg19.

Rerun: the Tophat jobs to use hg19 instead, then the derivative Cufflinks, Cuffmerge, and Cuffdiff jobs.

Everything else in your procedure looks great!

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson24k
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