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  • about bwa aln parameter tuning questions

    Hi guys,
    I'm using bwa to align solexa short reads (32 bp) to the reference genome. There are a couple of parameters for 'bwa aln', some of which I can't understand well. Could someone kindly help me fix some of my concerns as follows?

    The default values for parameters in bwa aln are as follows: aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -l inf -k 2 -t 1 -M 3 -O 11 - E 4

    In regards to bwa aln -n, the default value for -n is 0.04, is there anyway I can know the maximum edit distance ? Why is the default value for -n set as 0.04?

    In regards to -o, the default value for -o is 1. why is just one gap open allowed in one query sequence in the default setting?

    In regards to -e, the default value -e is -1. why is gap extention not allowed in one query sequence in the default setting?

    In regards to -l, the default value for -l is inf. why is seeding disabled in the default setting?


    When I use bwa aln, do I need to tune the parameters or just use the default setting for these parametersl? If the parameters are needed to be tuned, how should I tune these parameters?

    Could anyone kindly give me some suggestions?

    Thank you very much!

    Best

    Jing

  • #2
    I would like to know as well!!

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