rna-seq read distribution

wenhuang · 06-15-2010, 09:18 PM

I first posted the following thread at the RNA-seq sub forum. I found this place is much more popular

Hi,

I wonder how reads mapped to the genome (contiguously or to junctions) are distributed.

My own experience has surprisingly high fraction mapped to introns (over 30% of reads mapped to known genes). There could be many explanations:

1) pre-mRNA
2) DNA contamination, which I expect to be relatively uniform across all genes, but not in my case. But I found over 15% of mapped reads were to the mitochondrial genome. Well, it does contain genes (especially rRNA and tRNA), so not all of the reads may be from DNA. But I am not sure what this number really means.
3) erroneous mapping
4) novel exons
5) splicing that retains introns
etc.

Of course, introns are much longer, so if you count reads per unit length, the fraction goes down.

There are also conflicting evidence in the literature:

The Mortazavi (2008) paper reported 4% intronic reads and 93% exonic, while Marioni (2008) had a similar number (32% of reads mapped to genes are intronic) with what I have seen.

I am wondering what people on this forum have seen in their experience.

Thanks!

Wen

ECO · 06-17-2010, 10:07 AM

Please don't crosspost. Original thread is here:

http://seqanswers.com/forums/showthread.php?t=5519

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06-15-2010, 09:18 PM	#1
wenhuang Member Location: Raleigh, NC Join Date: Feb 2010 Posts: 30	rna-seq read distribution I first posted the following thread at the RNA-seq sub forum. I found this place is much more popular Hi, I wonder how reads mapped to the genome (contiguously or to junctions) are distributed. My own experience has surprisingly high fraction mapped to introns (over 30% of reads mapped to known genes). There could be many explanations: 1) pre-mRNA 2) DNA contamination, which I expect to be relatively uniform across all genes, but not in my case. But I found over 15% of mapped reads were to the mitochondrial genome. Well, it does contain genes (especially rRNA and tRNA), so not all of the reads may be from DNA. But I am not sure what this number really means. 3) erroneous mapping 4) novel exons 5) splicing that retains introns etc. Of course, introns are much longer, so if you count reads per unit length, the fraction goes down. There are also conflicting evidence in the literature: The Mortazavi (2008) paper reported 4% intronic reads and 93% exonic, while Marioni (2008) had a similar number (32% of reads mapped to genes are intronic) with what I have seen. I am wondering what people on this forum have seen in their experience. Thanks! Wen

06-17-2010, 10:07 AM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Please don't crosspost. Original thread is here: http://seqanswers.com/forums/showthread.php?t=5519