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  • #1

    ssaha2 with 454 Junior

    Hi

    I want to align my 454 Junior dataset with ssaha2.My command shell is:

    /share/apps/ssaha2_v2.5.3_x86_64/ssaha2 -rtype 454 -output sam -outfile MID2/454Reads.MID2.sam -save hg19 MID2/454Reads.MID2.fastq

    In the Sam output many of the reads have 255 quality value, so haven't any report of quality value. Then I do a Indels calling and I can't see any indels because I lost many informations....

    How I can process that values ​​quality? Why those value?

    Thanks
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