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  • -A option in bwa

    I've been trying to trim reads in prinseq then align them with bwa. I encountered a problem where bwa aln would get hungup on "align unmapped mate". This thread told me to use the -A option, which apparently disables Smith-Waterman mate rescuing. This solved the problem, but I don't know what, if any, effect this will have downstream (eventually they will be made into a nexus file and used in splitstree).
    Related question: bwa has -q trim option (for which the man page is indecipherable), how does this differ from trim_qual_right in prinseq? i.e. can i avoid using prinseq and the -A option altogether

    In case you're wondering, here is the command I used for prinseq, where $read2 is the file and $Trim is the quality score (I've been using 28):
    perl /Users/chsfredrick/data/prinseq-lite-0.19.3/prinseq-lite.pl -verbose -fast\
    q $Read2 -trim_qual_right $Trim

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