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  • blasr read length filter?

    Hey folks,

    I'm working with aligning some pacbio reads to a reference and have a question about blasr that I can't seem to figure out from the documentation. What I want is to only map the corrected reads which are longer than 3kb, to try to avoid spurious mismapping errors in repeat/transposase regions.

    The flag -minReadLength doesn't behave as I would expect it to though. When I peak at the results by running the following:

    head -5000 blasr.sam | awk '{if ($1 ~/@.*/) next; else if (length($10) < 3000) print length($10);}'

    I see that loads of alignments that are shorter than 3k which leaves me puzzled about a few things.
    • Anyone know what this flag actually does?
    • Am I missing something about what that tenth sequence field in the sam file means?
    • The default behavior is to not clip the alignments, so why are do I see alignments shorter than the shortest read I'm aligning? Shouldn't it only be reporting full length alignments?


    Thanks for your thoughts!
    Lizzy
    Last edited by ewilbanks; 07-17-2014, 08:20 AM.

  • #2
    The -minReadLength sets the minimum length of the reads getting aligned, not the minimum alignment length. Blasr finds best local alignment between a read and a reference, it does not align the entire read to the reference.
    To align, and only report alignments above a certain length you can use the pbalign wrapper to blasr, https://github.com/PacificBiosciences/pbalign also part of SMRT Analysis. Or, for aligning low error corrected reads Mummer may be a better option.
    Richard.

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