Hello Francisc, The Clip tool is sourced from the FASTX-tool kit, so specific edge-case behavior should be tested out or directed at the team that developed the tool at: http://hannonlab.cshl.edu/fastx_toolkit/index.html http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_clipper_usage On 1/9/12 4:33 AM, Fransisc Raul Kantor wrote:

Hi

We're a bit confused about exactly how the adaptor clipping tool works. Is there some documentation that describes how it does the clipping? In the clipping example given on the Galaxy page for "Clip adapter sequences" (the adaptor is CTGTAGGCACCATCATTATTTATATAA ):

* How large a substring of the sequence must the adaptor be in order for it to be clipped? E.g., if the sequence is ATGGACTCTG, it seems to clip the terminal CTG, but it doesn't clip if CTG appears somewhere in the middle of a sequence.

This is true for 3' clipping, because the adaptor leads with a CTG and the sequence ends with a CTG. The orientation is correct and the sequence's terminal CTG is clipped.

* Does it clip if, say, the middle part of the adaptor appears somewhere in the middle of a sequence, and if so, how long must it be before it clips?

Clipping off or introducing mismatches at the ends of an adaptor (up to 3 in a 10 base adaptor) still found and clipped in my test. More along these lines should narrow down the criteria or the tool authors can clarify. Best wishes, Jen Galaxy team

Thank you, Francisc Raul Kantor

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