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 On 4/17/12 11:15 AM, Xianrong Wong wrote:

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

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