What is the difference between the "match score", the mapping quality score under the tmap mapping pipeline

Question

[BioinfoNovice]

Hi,

I'm a newbie in Genomics. I have been using tmap for aligning reads obtained from an Ion Torrent platform. I'm trying to understand as much as possible the significance of the parameters. I have noticed that, for tmap, there are several options for aligning and filtering the alignments. I'm confused about the significance and difference between them.

Apparently, in tmap, there is an option to set a "match score" (set at 1 by default) and also another option to set a minimum of "alignment score" for filtering alignments, there is also another option for filtering alignments according to mapping quality threshold.

I'm kind of really confused about all these parameters because, for me, they are all the same.

If anybody could explain me clearly, I would be really grateful.

Answer 1

[Ram]

This is my understanding of these terms in general:

1. Match score: Score awarded for a base in a sequence matching a base in another sequence
2. Alignment score: Cumulative score of the bases of a sequence matching the bases of another sequence (more this score, better the alignment, if all else equal)
3. Mapping Quality score: Probability that the shorter sequence is mapped to the right spot on the longer sequence.

Maybe this can help you - it's based on a different tool, but the concept is the same.

http://biofinysics.blogspot.com/2014/05/how-does-bowtie2-assign-mapq-scores.html

[BioinfoNovice]

Thank you very much ! Without knowing all the details, it seems much clearer to me now.

[Ram]

Glad to help :) We're all learning here.