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Old 09-05-2013, 04:05 PM   #6
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Location: Bioinformatics Institute, SPb

Join Date: Jul 2012
Posts: 151

Originally Posted by sqcrft View Post
check this:


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").

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