Hello!
I am using Mosaik Aligner on 2x100bp paired end reads;
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:
I am now seeing things like..
Anyone know what those would all be about?
I am using Mosaik Aligner on 2x100bp paired end reads;
-mm <mismatches> the # of mismatches allowed
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
G:Z:ZGL39GTJ7H8 NM:i:9 MD:Z:84^T1G1T0T1T0T1T0G1T