Question: How to make Bowtie2 align a specific number of nt
0
gravatar for dchalagarcia
3 months ago by
dchalagarcia0 wrote:

Hi,

I am trying to align some tumor miRNA sequencing data to a viral genome using Bowtie2. In order to achieve the results I need, I need for Bowtie2 to only align a certain number of nt to my reference genome. Is there any way to tell Bowtie2 to only align the first 17 nts to my genome and ignore the last 5?

Thank you!

options settings bowtie2 input • 146 views
ADD COMMENTlink modified 3 months ago by y.hoogstrate460 • written 3 months ago by dchalagarcia0
1
gravatar for y.hoogstrate
3 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 wrote:

-3/--trim3 <int> trim <int> bases from 3' (right) end of reads

ADD COMMENTlink written 3 months ago by y.hoogstrate460
1

Find this option on the Bowtie2 tools form at:

  • Select analysis mode > 2. Full parameter list

  • Do you want to tweak input options? > Yes

  • Trim that many bases from 3' (right) end of each read before alignment (notes) -3/--trim3; default=0

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson24k
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