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  • Nandita
    Junior Member
    • Feb 2013
    • 2

    bwa flag 20

    I am using bwa on a paired-end fasta input file. Half of the mapped reads (flag not equal to 4) are mapped in reverse direction (flag = 16) and half are mapped with flag = 20. None have flag =0. Does anyone have a clue how this could happen?
  • swbarnes2
    Senior Member
    • May 2008
    • 910

    #2
    Maybe there was an instrument problem during the first read, causing the first read to have too many errors to map?

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