SEQanswers - View Single Post - Meaning of Negative Alignment Score in BOWTIE2 output

foolishbrat · 01-29-2014, 01:02 AM

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?

01-29-2014, 01:02 AM	#3
foolishbrat Member 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.