MAQ Scores & Quantify maq alignments?

[AnamikaDarwin]

Hello,

Is there a way to discern how well reads are aligning to a reference assembly using the mapping quality scores?

Thanks,
AnamikaDarwin

[somaye]

maq and bwt

hello,is any one help me for learning better maq and bwt alighnment. i want study about it ,but cant finde good sorce for it..

[dpryan]

They have published papers and freely downloadable source code...

[somaye]

do you have a book or ppt about it???

[dpryan]

There won't be a book on things like this. Perhaps you can find a ppt file somewhere (try slideshare).

[GenoMax]

Wikipedia (hopefully accessible from Iran) has good explanation of Burrows-Wheeler transformation: https://en.wikipedia.org/wiki/Burrow...eler_transform

Here is a useful deck of slides about alignments: http://evomicsorg.wpengine.netdna-cd...cture-2-v3.pdf