Hello. I'm having issues with Cuffdiff and can not figure out why. The program says the read order has to be the same but I ran all of then with Samtools sort -n to make sure and still having that issue.
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You need to sort by coordinate, not by name (remove the -n flag). The header of the bam should look something like this afterward:
@HD VN:1.0 SO:coordinate -
So do I sort the bam files using @HD VN:1.0 SO:coordinate with samtools?Originally posted by Brian Bushnell View PostComment
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No that is how the first header line should look after sorting.
Just remove -n option when you sort with samtools like Brian said.Comment
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You can check the headers of the BAM files with samtools view.
Code:samtools view -H fileName.bam
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