SEQanswers - View Single Post - Bowtie Paired-end options

days369 · 08-06-2010, 09:51 PM

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
--------------> -------------->
===============================================

OR

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

08-06-2010, 09:51 PM	#3
days369 Junior Member 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 --------------> --------------> =============================================== OR =============================================== <-------------- <-------------- read1 read2