TopHat 2.0.8: "Order of reads in BAMs must be the same", even AFTER Samtools Sort

[sindrle]

Hi!
I have run all my FASTQ files with the same setting (but different computers), the first one with a .GTF file (UCSC), the others with the .GFF version (turned on the transcriptome setting on the first run).

First I tried to run Cuffdiff 2.1.1, but got "Order of reads in BAMs must be the same" error.

I then tried Picard sort BAMs, after coordinates, did not work, so I deleted the files.

I then tried Samtools sort on all the BAMs, but I STILL get the same error.

Anyone knows??

[dpryan]

If you run cuffdiff on all but the first one, does it work or produce the same error? You might compare the headers of the first file and one of the others. Presumably they're different.

[sindrle]

Yes, thats it..

So, I must re-run with the .GFF then? Or is it a faster way?