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Old 01-29-2011, 09:31 PM   #1
gfmgfm
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Default different number of reads mapped to plus strand and minus strand

Hello all,

I have data of capture (sure select) followed by Illumina sequencing.
I see that I have more reads on the minus strand compared to the plus strand for example, for a certain position:
33 reads mapped to the plus strand and 96 reads mapped to the minus strand
88 reads mapped to the plus strand and 115 reads mapped to the minus strand

Does anyone has explanations for that?
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Old 02-03-2011, 07:22 AM   #2
seb567
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Quote:
Originally Posted by gfmgfm View Post
Hello all,

I have data of capture (sure select) followed by Illumina sequencing.
I see that I have more reads on the minus strand compared to the plus strand for example, for a certain position:
33 reads mapped to the plus strand and 96 reads mapped to the minus strand
88 reads mapped to the plus strand and 115 reads mapped to the minus strand

Does anyone has explanations for that?
DNA fragmentation is random, and so is cluster generation.

Did you look at the entire set of mapped reads or just a few ?

Last edited by seb567; 02-03-2011 at 07:26 AM. Reason: Clarity
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Old 02-03-2011, 10:26 AM   #3
gfmgfm
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Hi,

Thanks for the reply.

I looked at 2 parameters:
1. The number of reads mapped (on targets) - on plus strand and on minus strand:
For some samples it is the same, for many samples it is very different (~x2).
2. For each target base - I looked at a histogram of the number of reads mapped to that base on the plus strand divided by the total number of reads mapped to that base. It seems that there is some bias - and that there are bases that are covered only or mainly by one of the strands.
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