Question: Adaptor Trimming
gravatar for Soetkin Versteyhe
7.1 years ago by
Soetkin Versteyhe30 wrote:
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<http:""/> [cid:image001.gif@01CC9E39.FE2E3F70]
galaxy • 1.2k views
ADD COMMENTlink modified 7.1 years ago by Jennifer Hillman Jackson25k • written 7.1 years ago by Soetkin Versteyhe30
gravatar for Jennifer Hillman Jackson
7.1 years ago by
United States
Jennifer Hillman Jackson25k 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
ADD COMMENTlink written 7.1 years ago by Jennifer Hillman Jackson25k
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 REPLYlink written 6.6 years ago by Xianrong Wong90
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: Hopefully this helps, Jen Galaxy team -- Jennifer Jackson
ADD REPLYlink written 6.6 years ago by Jennifer Hillman Jackson25k
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