I have mapped reads to a reference using tophat/bowtie. I then use the output from tophat with cufflinks... and I get the following error "sort order of reads in BAMs must be the same."
I have tried sorting my tophat output with samtools... but that still doesn't work.
I am confused because I am only using 1 BAM file... so I do not understand what it is comparing my BAM file to that it thinks the sort orders are different.
Anyone know about this? I have seen the error posted in different threads but those are dealing with cuffmerge or cuffdiff which would be joining or comparing multiple BAM files.
I have tried sorting my tophat output with samtools... but that still doesn't work.
I am confused because I am only using 1 BAM file... so I do not understand what it is comparing my BAM file to that it thinks the sort orders are different.
Anyone know about this? I have seen the error posted in different threads but those are dealing with cuffmerge or cuffdiff which would be joining or comparing multiple BAM files.
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