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
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
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