Question: How to make Bowtie2 align a specific number of nt
0
gravatar for dchalagarcia
12 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 • 396 views
ADD COMMENTlink modified 12 months ago by y.hoogstrate460 • written 12 months ago by dchalagarcia0
1
gravatar for y.hoogstrate
12 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 wrote:

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

ADD COMMENTlink written 12 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 12 months ago by Jennifer Hillman Jackson25k
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