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  • Cuffdiff issue: Sort order of reads in BAMS must be the same

    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.


  • #2
    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

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    • #3
      Originally posted by Brian Bushnell View Post
      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?

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      • #4
        No that is how the first header line should look after sorting.

        Just remove -n option when you sort with samtools like Brian said.

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        • #5
          You can check the headers of the BAM files with samtools view.
          Code:
          samtools view -H fileName.bam

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