how to calculate MAPQ value in the tophat

[feixue1039]

Hi,

I have mapped some RNA-seq reads back to genome with Tophat and found that a lot of reads in the output of Tophat have a MAPping Value of 255. As says in the SAM specification file , a value 255 indicates that the mapping quality is not available. I wonder that in what case a read will be allocated a MAPQ value of 255 ? Does it mean that this read don't align the genome well?

I hope I have made the question clear to you all. Any reply will be appreciated.Thanks in advance!

feixue1039

[me_myself_andI]

Related and up to now also unanswered post:
http://seqanswers.com/forums/showthread.php?t=10594

[sqcrft]

some people say 255 means uniquely-mapped. but I can't find an source for that.

[sqcrft]

despite the sam format specification, 255 means no mapq

[sqcrft]

check this: http://user.list.galaxyproject.org/a...td4366680.html

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

[apredeus]

Originally Posted by sqcrft

check this: http://user.list.galaxyproject.org/a...td4366680.html

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.

This actually does not seem to hold upon checking (or at least not anymore). In Tophat 1.4.1, there is no mapping quality of 2. I've looked at a large number of BAM files and it seems that the qualities are as follows:

255 = unique mapping
3 = maps to 2 locations in the target
1 = maps to 3-4 locations
0 = maps to 5 or more locations (up to the number defined in "--max-multihits").

cheers