Adaptor Trimming

Question: Adaptor Trimming

7.1 years ago by

Hi! Does anyone know if it is possible to trim sequencing adaptor sequences away in Galaxy? Thanks! Soetkin Versteyhe, PhD PostDoc University of Copenhagen Faculty of Health Sciences The Novo Nordisk Foundation Center for Basic Metabolic Research Integrative Physiology Blegdamsvej 3B 2200 Křbenhavn N Denmark PHONE +45 35337116 soetkin.versteyhe@sund.ku.dk http://sund.ku.dk http://metabol.ku.dk<http: metabol.ku.dk=""/> [cid:image001.gif@01CC9E39.FE2E3F70]

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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by Soetkin Versteyhe • 30

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Soetkin, The FASTX-toolkit added into Galaxy has a tool for this. Look under "NGS: QC and manipulation -> FASTX-Toolkit for FASTQ data -> Clip adapter sequences". If this tool does not do exactly what you want, use the "Options -> Tool search" (top of left tool panel) and enter "trim" to see the alternatives. Hopefully one of these options will work out for you, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

Dear all, I'm trying to clip adapter sequences off the ends of my sequencing reads. I tested the tool by purposefully adding parts of the adapter sequence or the full adapter sequence to the 3' end. The tools is amazing in detecting these sequences. However, I encountered some problems. On top of detecting my adapter sequence I found that unrelated sequences are sometimes trimmed off at the 3' end. For example the sequence "TATCCACGTGCTC" was trimmed off even though it does not match the adapter sequence GATCCTCGGCCGCGACC at all. Is there a way to increase the fidelity of the tool? Any comments will be appreciated! Thank you! Best Regards, Jose

ADD REPLY • link written 6.6 years ago by Xianrong Wong • 90

Hi Jose, These sequences do align, although I agree somewhat loosely. Perhaps a desired match, considering the orientation and other factors? one TATCCACGTGCTC---- two GATCCTCGGCCGCGACC **** ** * * The Clip tool comes from the FASTX-Toolkit and has the standard options implemented in Galaxy (as you probably noticed, there are no options to tune the actual "match" criteria). If you would like to share some of the corner cases or suspected problems your found with the author, the home page and contact link is: http://hannonlab.cshl.edu/fastx_toolkit/ Hopefully this helps, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k

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