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-   -   Unique and repeat Hits (http://seqanswers.com/forums/showthread.php?t=2113)

pfranchini 07-15-2009 09:04 AM

Unique and repeat Hits
 
Hi,
In which way I can filter the information of unique and repeat hits of the reads to the reference with Maq? There is a way to obtain a global statistic of the mapping? Thanx

P

nilshomer 07-15-2009 09:51 AM

Quote:

Originally Posted by pfranchini (Post 6588)
Hi,
In which way I can filter the information of unique and repeat hits of the reads to the reference with Maq? There is a way to obtain a global statistic of the mapping? Thanx

P

You can use the mapping quality. Zero mapping quality means there were multiple equally likely mappings, and greater than zero means there was a most likely mapping found. If you want some general mapping statistics, you could convert your .map file to the SAM/BAM format and use the samtools "flagstat" command.


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