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Old 07-28-2009, 01:10 PM   #1
Location: California

Join Date: Jul 2009
Posts: 46
Default maq map/match settings in colorspace

Hi all.
I just started working with MAQ, SOLiD, and Illumina software/hardware this month and had a hard time finding answers to these questions (maybe i missed them!)

First, how does MAQ handle the mismatch threshold when mapping SOLiD reads with MAQ? Setting -n 3 would allow for 3 mismatches in the firs 24 bp of the read in the mapping when using Illumina data. Does setting -n 3 -c allow for three mismatches in colorspace, or 1.5?

also, the maq manual suggests -n INT can handle numbers >3 but in practice my installed maq versions 0.7.1 will only run -n <=3.

lastly, SOLiD matepairs are in the FF orientation while Illumina matepairs are in the FR/RF orientation. if i switch the orientation of one of my SOLiD matepairs in fastq format, can i get paired end alignments of SOLiD sequence using MAQ?

Thanks for your help.

[update] I think the 2008 thread here may answer my first and third questions. Namely that -n 3 in colorspace doesn't mean 3 neighboring sets of colorspace mismatches but rather any 3 SINGLE colorspace mismatches; and MAQ can run SOLiD matepairs as matepairs rather than single end reads. Second question still needs answering because I'd like to run -n 4 or -n 5 to increase my mapping efficiency.

Last edited by der_eiskern; 07-28-2009 at 02:19 PM. Reason: potentially found answers to some of these questions
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