SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Read qualities in a sam file produced by BWA. north_zeb Bioinformatics 7 06-04-2013 08:36 AM
short read qualities for various NGS machines sweet_dna_girl Bioinformatics 4 05-05-2011 05:00 PM
read-qualities lost in Mosaik-processing tczy Bioinformatics 4 05-17-2010 08:31 AM
Converting ABI colorspace qualities into base qualities szilva Bioinformatics 7 04-01-2010 11:38 PM
TopHat mapping qualities dychiang Bioinformatics 0 10-20-2009 01:44 PM

Reply
 
Thread Tools
Old 07-15-2013, 02:58 PM   #1
mmanhart
Member
 
Location: United States

Join Date: Jan 2013
Posts: 11
Default How does bowtie2 calculate read mapping qualities?

I'm wondering exactly how bowtie2 calculates the read mapping qualities shown in the output SAM file. The documentation makes it very clear how the internal mapping score is calculated, and how you can customize it (e.g., setting various penalties for mismatches and indels), and it says that this is used to calculate the actual mapping quality, but I can't find anywhere that shows exactly how the mapping quality is ultimately calculated.

Does it use the same heuristic formula as in MAQ? Here's the paper I know about:

Li H, Ruan J, Durbin R. (2008) "Mapping short DNA sequencing reads and calling variants using mapping quality scores." Genome Res. 18:1851--1858.

Many thanks for your help,
Michael
mmanhart is offline   Reply With Quote
Old 07-20-2013, 03:41 PM   #2
mmanhart
Member
 
Location: United States

Join Date: Jan 2013
Posts: 11
Default

Can anyone here help me out? I would really appreciate it!

Thanks,
Michael
mmanhart is offline   Reply With Quote
Old 07-21-2013, 09:38 PM   #3
sdriscoll
I like code
 
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438
Default

the MAPQ isn't super informative. only got to do with the uniqueness of the alignment where higher scores means more unique. so it's probably a -10*log10(p) where p is some probability of the alignment being unique. I don't know what their probability formula is, however. if this is what they do then the formula isn't a straightforward one like they use in Tophat and STAR.
__________________
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
sdriscoll is offline   Reply With Quote
Old 07-22-2013, 07:37 AM   #4
mmanhart
Member
 
Location: United States

Join Date: Jan 2013
Posts: 11
Default

I know what you're saying --- that's all I can find documented in the Bowtie2 manual and publisher paper. However, I would indeed like to see the explicit formula used to calculate this. I find it really striking that it is not documented clearly --- many downstream filters work on mapping quality, so it should be very improtant to know exactly what goes into it.
mmanhart is offline   Reply With Quote
Old 07-23-2013, 11:27 PM   #5
sdriscoll
I like code
 
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438
Default

You're right..they should at least put it into words so one can know what they are doing.
__________________
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
sdriscoll is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:02 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO