Question: Trimming sequences with homology parameters
0
gravatar for eddreuzy
2.9 years ago by
eddreuzy0
France
eddreuzy0 wrote:

Hello,

I am processing single-end illumina reads coming from a PCR library. 

I know the flanking sequences of my reads and need to: 

- select the sequence that contain the 5' constant region (with >90%homology for the 39 first nt; 100% for the last 3nt) and remove that sequence

- remove the 3' constant sequence when it is present

All the tools I found do not offer mismatches/gaps parameters, or can not be inserted in a workflow.

Do you know what tools I can use to do that ? (I used to do it with flexbar but it cannot be integrated into workflows),

 

Thanks for your help !

Edouard

 

 

galaxy trimming • 577 views
ADD COMMENTlink written 2.9 years ago by eddreuzy0
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