bowtie --best, what exactly does it mean?

Question

[slapiiv]

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

[ATpoint]

Potential answers on SeqAnswers.

[slapiiv]

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.

[GenoMax]

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

Answer 1

[Charles Warden]

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)."

[slapiiv]

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