Re: [Samtools-devel] Differenciating uniquely mapped reads from "best score" reads

[Benjamin B. <be...@gm...>]

It's true that it might be a bit aligner-specific, but that does not negate it's primary use case which would be to determine simply whether  or not *any* other strong matches exist. You could try to give it a more concrete interpretation (any matches with a 5% or more probability of being correct, any matches within an edit distance of N from the best match), but it would be difficult or more likely impossible to get aligners to comply with this.  In practice, any aligner capable of returning multiple hits has to have some cutoff, and this would be the same cutoff used for the proposed "numHits" field.

ben.


On Dec 11, 2009, at 2:03 PM, Paul Anderson wrote:

> On Fri, Dec 11, 2009 at 3:13 PM, David Rio <dri...@gm...> wrote:
> 
>> I would like to suggest an extra tag in the SAM spec to differentiate
>> uniquely mapped reads
>> from "best score" reads. What I would suggest is adding an extra tag
>> that is either 0 for
>> uniquely mapped reads or # where # is the number of other hits for that read.
>> 
>> What do you guys think?
> 
> I think it is misleading, since depending on the aligner, or the
> settings of the aligner, you are going to get different answers.
> 
> In many index based aligners, (e.g. KARMA), if you use a smaller
> index, you will tend to get more possible matches.
> 
> That said, KARMA will write the number of locations it evaluated for a
> single ended read, but like Goncalo suggested, I think the quality
> score is really what you're looking for.
> 
> The mapping score, if aligners are doing a good job computing it,
> should be moderately comparable across aligners, since it has a
> mathematical basis in reality.
> 
> Paul
> 
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