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Old 08-06-2010, 09:51 PM   #3
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Location: US

Join Date: Aug 2009
Posts: 8

kmcarr, thanks so much. your reply is really helpful.

I guess that my reads should be produced using the Illumina paired end protocol, so most of them are in --fr orientation.

But a small portion of the paired-end reads are in --rf/--ff orientation, because they can be mapped with those two options. Some are even in an orientation as illustrated below. I guess they are different from the -ff orientation, because read2 is 5' to read1.

Do you have any idea why the same illumina paired-end protocol can generate some reads that is not in -fr orientation? or Do you meet this problem before?

read2 read1
--------------> -------------->


<-------------- <--------------
read1 read2
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