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


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 4 months ago • written 4 months ago by ritar10

Hello ritar!

Questions similar to yours can already be found at:

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ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
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