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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