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
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