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  • XS tags in hisat2 alignment

    Hi,

    I had some troubles running Cufflinks with input mapping from HIsat2 (sam/bam).

    Cufflinks man page says that input file should be sorted and contain XS tags. To add the tags, I specified --dta-cufflinks as parameter in for the alignment, following Hisat2 man page. With this parameter, supposedly, " [...] HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.". However, this tag does not appear in every line (read) of the generated bam file.

    Is this possible and/or expectable? If you ever encountered this issue before, how could you fix it?

    I was thinking to first generate a file like this prior to launch of Cufflinks run:
    Code:
    samtools view hisat2.sorted.bam | egrep 'XS:A:-|XS:A:+' > XS-Tagged.sorted.sam
    What do you think?
    Last edited by dovah; 08-05-2016, 05:23 AM.

  • #2
    IIRC, Cufflinks only requires XS tags for spliced alignments.

    Comment


    • #3
      Ha ok, so it should be fine. Have you ever used Cufflinks on bam file generated by Hisat2 by the way? Because it is taking a huge lot of time. I can spot CPU usage (~99%) but no tmp files in the working directory.

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      • #4
        Originally posted by dovah View Post
        Cufflinks ... is taking a huge lot of time.
        Sounds like it's working as expected

        Seriously, though, sometimes that can happen if you have super-high coverage over certain reasons... in which case filtering out those regions can help (if you're not interested in them).

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        • #5
          oh thanks Brian. I was so worried :P

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