Unique and repeat Hits

pfranchini · 07-15-2009, 09:04 AM

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

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.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
how to extract unique hits from a sam file	gfmgfm	Bioinformatics	10	07-07-2019 08:33 AM
Bowtie call to get unique, multi-hits and nonmatching reads	PFS	Bioinformatics	3	07-07-2019 08:18 AM
unique hits	arrchi	Bioinformatics	7	06-01-2011 08:53 AM
Regarding Unique reads, Unique alignments	sridharacharya	RNA Sequencing	2	09-20-2010 06:39 AM
Unique VS Non-Unique read analysis	samt	Bioinformatics	2	09-29-2009 10:44 AM

07-15-2009, 09:04 AM	#1
pfranchini Member Location: Cape Town Join Date: May 2009 Posts: 19	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