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The exact meaning of -act and -mmp in MOSAIK alignment #18

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haoecust opened this issue Oct 21, 2015 · 0 comments
Open

The exact meaning of -act and -mmp in MOSAIK alignment #18

haoecust opened this issue Oct 21, 2015 · 0 comments

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@haoecust
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I currently using Mosaik to align 100 bp pair-end raw reads of WGS to human reference. I'm very confused on the two parameters in mosaik.
-act (alignment candidate threshold), in mosaik document, it said it means the the minimum length of bases in each seed cluster. I'm still don't totally understand it. What's the meaning of seed cluster here?

-mmp (maximum mismatch percentage): "specifies the maximum percentage of the read length that are allowed to be errors."
As I know, the mismatches parameter (-mm) has already been set at default:4. I wonder to know the difference between the -mmp and -mm. Does -mm means the mismatches in each seed? -mmp indicate the mismatches in the whole read?

Thanks very much.

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