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  • some quesiton on "bwa index"

    Hi everybody:

    supposed that:
    1. reference file: hg19.fa
    2. solexe data: 1.fq.gz

    and i do bwa index and aln like the follow:

    bwa index -a bwtsw hg19.fa

    bwa aln -t 2 -n 2 -o 1 -e 5 -q 20 hg19.fa 1.fq.gz >1.sai 2>1.sai.sterr

    am i right?
    and what's the difference between the formal hg19.fa and the hg19.fa indexed.thank you very much. yours help is greatly appreciated.Best wieshes.

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