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Old 01-29-2014, 01:02 AM   #3
Location: South East Asia

Join Date: Nov 2008
Posts: 44

Thanks, two more questions:

So if I remove -k1 that means for each read it will output only 1 best position, which doesn't mean it's uniquely mapped, am I right?

If so how can I determine the uniquely mapped reads from the parameter or the SAM output?
By looking at MAPQ=255?

Last edited by foolishbrat; 01-29-2014 at 01:09 AM.
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