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Old 04-12-2010, 08:58 AM   #1
sanush
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Location: san diego

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Default Too many reads mapping towards intronic region

Hi all
We just finished our first RNA seq experiment in SOLiD platform and used partek to map our reads. We see that only 30% maps to exonic and remaining of our reads mapping to intronic and intergenic regions (30% on each regions).

We are trying to figure out the reason for high numbers mapping to intronic regions. Any advice.

Thanks
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Old 04-13-2010, 10:10 AM   #2
steven
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FYI, it is not the first time i see some important discrepancy in the proportion of "exonic" reads. For instance 93% (Mortazavi et al), 39% (Li et al, PNAS 2008) or 33% of mapped reads (Tang et al, 2009, Nat.Met).
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