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I am trying to feed cuffdiff accepted_hits.bam files from both tophat1 and tophat2. It works just fine on either files alone, but crashes when i mix.
The error is :
Error: sort order of reads in BAMs must be the same
It does not help to feed all files through either "sort" (as recommended in the cufflinks manual) or "samtools sort".
When I look at the .sam versions, I notice that tophat2 adds a number of extra entries (to each line) between the qual scores and the end of each line.
Any ideas what the problem is/how to fix?
The error is :
Error: sort order of reads in BAMs must be the same
It does not help to feed all files through either "sort" (as recommended in the cufflinks manual) or "samtools sort".
When I look at the .sam versions, I notice that tophat2 adds a number of extra entries (to each line) between the qual scores and the end of each line.
Any ideas what the problem is/how to fix?