Hello,

This Galaxy wrapper is based on the FASTX-Toolkit tool by the same name. A link to the original is at the bottom of the tool's form in the UI. To see the Galaxy wrapper, it is in the source here: galaxy-central / tools / fastx_toolkit
https://bitbucket.org/galaxy/galaxy-central

Questions about the core tool can be directed to the tool author. Help with running a local Galaxy or tools in general is on the galaxy-dev@bx.psu.edu mailing list: http://wiki.galaxyproject.org/Support#Mailing_Lists

If you create a new wrapper with more options, please consider contributing it to the Tool Shed, as this tool is super popular and the option for 5' clipping has come up before. http://wiki.galaxyproject.org/Tool%20Shed

Take care,

Jen
Galaxy team


On 8/22/13 12:58 PM, William Yarosh wrote:
Thanks,

I'm trying to figure out how to use these programs.

Do you know where I can get the source code for clip?  I think I can edit the program to look at the 5' end if I see it.

Will

On Aug 22, 2013, at 3:19 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hello,

The "Clip" program only acts on the 3' end. In some cases, running "FastQC" to isolate adapter regions, then using a tool like "FASTQ Trimmer" or "Trim" will work (if the lengths are somewhat fixed).

Alternately, the tools "NGS: QC and manipulation -> Reverse-Complement or Manipulate FASTQ" will reverse compliment reads. For the second, the option is located in Manipulate Reads -> Manipulate on 'Sequence Content' -> Sequence Manipulation Type:. There are several options here, including trim again, but also "Reverse Complement".

Hopefully this helps!

Jen
Galaxy team


On 8/22/13 12:03 PM, William Yarosh wrote:
Hi,

I was using the clip program, but my adapters are on the 5' end.  Is there any way to use this program so it will clip the 5' end or a way to make all my reads the reverse complement and run it through this program?

Thanks
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/


-- 
Jennifer Hillman-Jackson
http://galaxyproject.org


-- 
Jennifer Hillman-Jackson
http://galaxyproject.org