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.goe...@emory.edu> To: "Li, Jilong (MU-Student)" <jl...@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-c60d17a6e...@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: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/
___________________________________________________________ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
