Question: Bowtie: Reporting one of multiple valid mapping locations
0
gravatar for Sander
4.7 years ago by
Sander20
The Netherlands
Sander20 wrote:

Dear Biostars,

I'm slightly confused by the way Bowtie reports reads that align to multiple locations. If I understand correctly from the manual, http://bowtie-bio.sourceforge.net/manual.shtml#reporting , by default only 1 alignment is returned (-k 1). But this may not necessarily be the best alignment, because then --best must be specified aswell. So is this a random or just a 'good' alignment? And what is the difference with -M 1? According to the manual this gives 1 random alignment from the best alignments, but is this not the same as -k 1?

Kinds regards,

Sander

bowtie mapping • 1.5k views
ADD COMMENTlink modified 4.7 years ago by geek_y10.0k • written 4.7 years ago by Sander20
0
gravatar for geek_y
4.7 years ago by
geek_y10.0k
Barcelona
geek_y10.0k wrote:

-k is not related to 'best' alignment. -k is related to multimapped reads. A read may map at various places with v.high quality/best mapping, but only one position is reported by default.

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by geek_y10.0k

So with -k 1, in the case that a read maps to various places, which position is reported?

ADD REPLYlink written 4.7 years ago by Sander20
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