[galaxy-user] Shortening sequences?

[Thomas Haverkamp]

Hi all,
Thanks for the answers,
I do see the Trim sequence tool on the galaxy test website, but when I  
run the tool on a small fasta file, it seems to crash constantly. Is  
that because it does not recognize my fasta file??
  Furthermore, I am not a programmer (have to become one, I guess) so  
I would like to try the FastX program. I will try that too.
Cheers
Thomas

On Sep 30, 2009, at 5:32 PM, Anton Nekrutenko wrote:

> Thanks Chris:
>
> This tool is already in Galaxy on the test site (http://test.g2.bx.psu.edu 
> ) under "NGS: QC and manipulation" section.
>
> a.
>
>
> On Sep 30, 2009, at 11:07 AM, Chris Cole wrote:
>
>> Hi Thomas,
>>
>> Unless you can code it yourself (it's a fairly trivial thing to  
>> do), I
>> would recommend the Fastx toolkit which includes a tool for this
>> (amongst many other things)
>> http://hannonlab.cshl.edu/fastx_toolkit/
>>
>> Cheers,
>>
>> Chris
>>
>> Thomas Haverkamp wrote:
>>> Hi All,
>>> I have a little how to do question and was hoping somebody knows  
>>> the answer?
>>>
>>> I have a metagenomic data set with reads of lengths between 100  
>>> and 1000
>>> bp. Now I want to create a dataset from my original dataset, with
>>> sequences of exact 200bp. I know I can use the filter tool to  
>>> extract
>>> all reads longer than 199bp from the original data set. But then I  
>>> want
>>> to cut off all the sequence bit that is longer than 200bp. so I  
>>> end up
>>> with only a dataset of exactly 200bp. Does anybody know how I can do
>>> that in Galaxy. I was thinking of some of the EMBOSS tools, but they
>>> only see the first sequence and not all the other sequences in my  
>>> Fasta
>>> file?
>>>
>>> Any ideas are welcome.
>>> Cheers
>>>
>>> Thomas
>>>
>>>
>>> Dr. Thomas H.A. Haverkamp
>>> Centre for Ecological and Evolutionary Synthesis (CEES)
>>> Dept. of Biology
>>> University of Oslo
>>> P.O. Box 1066 Blindern
>>> 0316 Oslo Norway
>>>
>>> Phone: +47 22 85 44 00
>>> Mobile: +47 48 09 49 32
>>> E-mail: thhaverk at bio.uio.no <mailto:thhaverk at bio.uio.no>
>>> Skype: Thomieh73
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> galaxy-user mailing list
>>> galaxy-user at bx.psu.edu
>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>>
>>
>> -- 
>> Dr Chris Cole
>> Senior Bioinformatics Research Officer
>> School of Life Sciences Research
>> University of Dundee
>> Dow Street
>> Dundee
>> DD1 5EH
>> Scotland, UK
>>
>> url: http://network.nature.com/profile/drchriscole
>> e-mail: chris at compbio.dundee.ac.uk
>> Tel: +44 (0)1382 388 721
>>
>> The University of Dundee is a registered Scottish charity, No:  
>> SC015096
>> _______________________________________________
>> galaxy-user mailing list
>> galaxy-user at bx.psu.edu
>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>
> Anton Nekrutenko
> http://nekrut.bx.psu.edu
> http://galaxyproject.org
>