Question: (Closed) How to get only paired end or single end uniquely mapped reads with Bowtie2?
0
gravatar for ritar
10 months ago by
ritar10
ritar10 wrote:

Hello,

I am using bowtie2 on galaxy to map ChIP-seq single end and paired end libraries to a reference genome. I want to be sure I get only uniquely mapped reads (for single end) or uniquely mapped paired of reads (for paired end). I don't want : reads mapping at multiple locations and being randomly assigned a location; reads mapping to multiple locations and being assigned all the locations. I really want proper uniquely mapping reads. And I need it because I am working with repeated sequences (I saw some posts that suggest we shouldn't care about multimapping but in my case, is kinda of important) Is this possible with bowtie2? I couldn't find it in the manual but again, I am not an expert.

Thank you

ADD COMMENTlink modified 10 months ago • written 10 months ago by ritar10

Hello ritar!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour