Question: bowtie --best, what exactly does it mean?
1
gravatar for slapiiv
10 months ago by
slapiiv50
slapiiv50 wrote:

Hi, everybody: I am using bowtie for aligning smallRNAseq reads against a genome reference, I am using --best because it is recommended for miRNAs, but as you may know the bowtie`s manual is not clear enough as we the beginners need. Does somebody know what does it exactly means?

 --best             hits guaranteed best stratum; ties broken by quality
mapping rna-seq bowtie • 323 views
ADD COMMENTlink modified 10 months ago by Charles Warden7.6k • written 10 months ago by slapiiv50
1

Potential answers on SeqAnswers.

ADD REPLYlink written 10 months ago by ATpoint30k
1

Thanks, the answer that I was looking for is: a strata is a set of alignments where mismatches occur at identical positions. For example, suppose there are two 1-mismatch hits. One with the mismatch at 7th position and the other at the 9th position. The two hits are in two different strata.

ADD REPLYlink written 10 months ago by slapiiv50
1

That is not what post #5 and #6 say in the SA thread linked above.

ADD REPLYlink written 10 months ago by genomax78k
1
gravatar for Charles Warden
10 months ago by
Charles Warden7.6k
Duarte, CA
Charles Warden7.6k wrote:

I had to look closely at the manual, but I think this explains that --best and --strata have different meanings, but I think it would have been helpful if there were some examples where -a wasn't added to report all alignments:

http://bowtie-bio.sourceforge.net/manual.shtml#reporting-modes

In other words, in their examples where all alignments are being reported with -a, I think --best is sorting the reported alignment order, and --strata is actually filtering for the hit with the fewest mismatches. However, otherwise the manual says "When --best is not specified, Bowtie may report alignments that are sub-optimal in terms of stratum and/or quality (though an effort is made to report the best alignment)."

ADD COMMENTlink modified 10 months ago • written 10 months ago by Charles Warden7.6k

Oh I see, bowtie is a bite confusing anyways, but I have undesrstand my specific doubt. Thanks.

ADD REPLYlink written 10 months ago by slapiiv50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1636 users visited in the last hour