Unique and repeat Hits

[pfranchini]

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]

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.