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Old 05-13-2011, 09:22 AM   #1
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Location: Valencia

Join Date: Feb 2011
Posts: 4
Default ssaha2 with 454 Junior


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?

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