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 <jen@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
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