Jeremy,
This is not strictly correct. Tophat/bowtie don't report mapping quality values that are as meaningful as BWA, but there is some information in the mapping quality values tophat reports. Tophat yields 4 distinct values for its mapping quality values (you can do a "unique" count on the mapping quality field of any SAM file from tophat to verify this):
255 = unique mapping
3 = maps to 2 locations in the target
2 = maps to 3 locations
1 = maps to 4-9 locations
0 = maps to 10 or more locations.
Except for the 255 case, the simple rule that was encoded by the authors is the usual phred quality scale:
MapQ = -10 log10(P)
Where P = probability that this mapping is NOT the correct one. The authors ignore the number of mismatches in this calculation and simply assume that if it maps to 2 locations then P = 0.5, 3 locations implies P = 2/3, 4 locations => P = 3/4 etc.
As you can clearly see, then MapQ = -10 log10(0.5) = 3; -10 log10(2/3) = 1.76 (rounds to 2);
-10 log10(3/4) = 1.25 (rounds to 1), etc.
-Kevin
Date: Tue, 7 Feb 2012 17:56:34 -0500
From: Jeremy Goecks jeremy.goecks@emory.edu
To: "Li, Jilong (MU-Student)" jl482@mail.missouri.edu
Cc: "galaxy-user@lists.bx.psu.edu" galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] about Mapping Quality
Message-ID: 84AF17B7-3317-43CF-92BA-C60D17A6E037@emory.edu
Content-Type: text/plain; charset="us-ascii"
Tophat/Bowtie does not yield mapping quality, so, as per the SAM spec, that field is set to 255, indicating that quality is unavailable.
http://samtools.sourceforge.net/SAM1.pdf
Best,
J.
On Feb 7, 2012, at 5:46 PM, Li, Jilong (MU-Student) wrote:
Hi all,
I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file,
the value of some mapping quality (the 5th column) is 255. What does it mean? And I found these reads which have mapping quality 255 mapped to unique place.
Thanks!
Victor
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
galaxy-user@lists.galaxyproject.org