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Old 09-15-2013, 10:36 PM   #4
Pengfei Liu
Location: Beijing

Join Date: Nov 2012
Posts: 16

so still some additional questions
1, I want to use the mapping results of bwa to do Differential expression analysis, what kind of reads should be kept?
1) mapping quality q>threshold(30 or 60), as you mentioned quality larger than 1 will exclude reads mapping to multiple positions
2) NM tag indicates the number of mismatch, so NM:i:0-5 might be used to restrict mismatch. ()
3) flag 99-147 or 83-163 to kept properly paired reads
are the above three suitable criteria?
Thank you!
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