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Old 11-05-2011, 04:57 PM   #1
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Location: British Columbia

Join Date: Jun 2011
Posts: 6
Default [Mosaik] - parameter settings


I am using Mosaik Aligner on 2x100bp paired end reads;
-mm <mismatches> the # of mismatches allowed
Does that mean mm in each pair member individually (assuming this), or the entire stretch? Any suggestions/wisdom on any other settings that people have out there would also be much appreciated!

Secondly, I have a question about the SAM output it creates:
Usually, in tophat, I could expect some of the following information at the end of each line in the SAM file:
NM:i:1 XS:A:+ NH:i:1
I am now seeing things like..
G:Z:ZGL39GTJ7H8 NM:i:9 MD:Z:84^T1G1T0T1T0T1T0G1T
Anyone know what those would all be about?
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