Thanks Geert,
This tool was in the back on my mind, but I couldn't find it last week for some reason!

Seung Hee - this is a very good choice, for use in a local or or cloud Galaxy.
http://getgalaxy.org
http://usegalaxy.org/cloud

I think I will close out the ticket below and point it to CutAdapt as a solution. A ticket to ask for this tool to be on Main is a distinct subject/issue - if someone wants to submit that request, the community can vote, team can priotitize, etc.
http://wiki.galaxyproject.org/Issues

The tool Peter mentions can also be examined. One may fit your needs better than the other,

Thanks!!
Jen
Galaxy team

On 11/25/13 6:03 AM, Geert Vandeweyer wrote:
You might also use ( / add to main) the CutAdapt tool, which is available in the main toolshed. It takes multiple adapters, allows 3/5/both side adapters, and is fast.

http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=User.username&operation=view_or_manage_repository&id=f19bc86bac946438

Best,

Geert

On 11/23/2013 03:19 PM, Peter Cock wrote:
On Fri, Nov 22, 2013 at 8:48 PM, Jennifer Jackson<j...@bx.psu.edu>  wrote:
Hi Seung Hee,

I know we discussed this on the other list, but I didn't point you to the
open development ticket to (potentially) extend the functions of the "Cut"
tool. This is not being actively worked on right now, but you can follow it
for updates if you want.
https://trello.com/c/CbFSHrU5

Others are still welcome to comment about what types of solutions they might
have to offer. There is no specific tool to do this on Main right now (or in
the Tool Shed, from my checks).http://usegalaxy.org/toolshed
This tool of mine might do what Seung Hee wanted,
but I have not tried it on very large Illumina datasets:

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip

Regards,

Peter
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Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
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