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  • Does bwa support SOLiD PE data?

    Hi,
    I have used 'bwa aln' and 'bwa sampe' for mapping Exome captured SOLiD PE reads.
    I am getting very low PE mapping % (29-35%) One of the notes on the 'bwa version 0.5.9-r16' says:
    Notes:
    1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.
    2. For reads shorter than 30bp, applying a smaller -o is recommended to
    to get a sensible speed at the cost of pairing accuracy.

    So my question is if bwa truly support SOLiD PE reads?
    If so, what parameters have to be modified ?
    The reads are F3 and F5, there is no R3.

    Do the version 0.5.9-r16 have changes to sampe that was posted by Brugger at bwa-support mailing list.

    CATEGORY TOTAL_READS PF_READS %_PF_READS PF_NOISE_READS PF_READS_ALIGNED %_PF_READS_ALIGNED
    FIRST_OF_PAIR 134520572 134520572 1 34 14456389 0.107466
    SECOND_OF_PAIR 134520572 134520572 1 17 82292274 0.611745
    PAIR 269041144 269041144 1 51 96748663 0.359605

    CATEGORY READS_ALIGNED_IN_PAIRS %_READS_ALIGNED_IN_PAIRS
    FIRST_OF_PAIR 10169637 0.70347
    SECOND_OF_PAIR 10169650 0.12358
    PAIR 20339287 0.210228



    Thanks
    VJ
    Last edited by 2007lab; 05-09-2011, 12:20 PM. Reason: bwa spelling

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