Unique VS Non-Unique read analysis

samt · 09-29-2009, 08:22 AM

I have been debating the it is more appropriate to use only uniquely mapping reads in analysis (transcript variation, expression, structural variation). I wanted to get feedback from other people and poll the consensus for analyzing rna-seq data.

If this has been discussed already, a paper link or thread would be helpful.

swbarnes2 · 09-29-2009, 09:49 AM

There was a recent Nature paper that mentioned uniqueness filtering...some commentary on it here:

http://www.massgenomics.org/2009/09/...an-exomes.html

the blog author's take: you should get rid of non-unique reads, but this is going to limit your max coverage of single end data to 2x the read length. With paired ends, since you can get fragments of multiple sizes, your max coverage can be a whole lot higher.

samt · 09-29-2009, 10:44 AM

much appreciated, there is some good insight in this paper. if you know of any other papers, link them also

Thanks

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
unique hits	arrchi	Bioinformatics	7	06-01-2011 08:53 AM
Help with Bowtie, only unique alignments	khb	General	1	12-16-2010 01:35 AM
Regarding Unique reads, Unique alignments	sridharacharya	RNA Sequencing	2	09-20-2010 06:39 AM
unique reads for downstream analysis	bioinfosm	Bioinformatics	3	07-07-2009 02:30 PM
unique regions...(MAQ)	Colorful_Seq	Bioinformatics	0	03-18-2009 05:17 AM

09-29-2009, 08:22 AM	#1
samt Member Location: NYC Join Date: Aug 2009 Posts: 14	Unique VS Non-Unique read analysis I have been debating the it is more appropriate to use only uniquely mapping reads in analysis (transcript variation, expression, structural variation). I wanted to get feedback from other people and poll the consensus for analyzing rna-seq data. If this has been discussed already, a paper link or thread would be helpful.

09-29-2009, 09:49 AM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	There was a recent Nature paper that mentioned uniqueness filtering...some commentary on it here: http://www.massgenomics.org/2009/09/...an-exomes.html the blog author's take: you should get rid of non-unique reads, but this is going to limit your max coverage of single end data to 2x the read length. With paired ends, since you can get fragments of multiple sizes, your max coverage can be a whole lot higher.

09-29-2009, 10:44 AM	#3
samt Member Location: NYC Join Date: Aug 2009 Posts: 14	much appreciated, there is some good insight in this paper. if you know of any other papers, link them also Thanks