sort order of reads in BAMs must be the same

[mcco...@molbio.mgh.harvard.edu]

      When I try to run Cuffdiff using an accepted_hits.bam file
outputted from TopHat 2.0.7 and another accepted_hits.bam file outputted
from TopHat 2.0.10, it will not work and I receive the error message:
sort order of reads in BAMs must be the same.

     If I run Cuffdiff with accepted_hits.bam files from TopHat 2.0.0 and
2.0.7, everything works fine.

     I am using Cufflinks 2.1.1 for all.

Matthew

[Shawn Driscoll]

That's strange.  Have you tried sorting them first?  Also...why are you using output from 4 different versions of Tophat?

If you take each BAM and run this...

samtools sort accepted_hits.bam accepted_hits.sorted

they should all be good.

[Javier C Alvarez]

Hi Matthew,

Did you resolve that problem? I have the same error message... Could you help me? Thanks

[Stephanie Gage]

Hi All,

Has anyone successfully resolved this problem? I've been troubleshooting, and troubleshooting....

Interesting information on the versions of TopHat. I've had success before, so perhaps it is something version related. Any tips would be appreciated.

Thanks!

SG