Hi all, Does anyone know if it is possible to trim/clip a sequence from the 5' end? Thank you. Best, Soetkin. Soetkin Versteyhe, PhD PostDoc University of Copenhagen Faculty of Health Sciences The Novo Nordisk Foundation Center for Basic Metabolic Research Integrative Physiology Blegdamsvej 3B 2200 København N Denmark PHONE +45 35337116 soetkin.versteyhe@sund.ku.dk http://sund.ku.dk http://metabol.ku.dk<http://metabol.ku.dk/> [cid:image001.gif@01CCA476.A4F86460]
Hi, with regard to the 5' clipping: On the main (usegalaxy.org) server: it is possible using the "NGS: QC and manipulation" => "Generic FASTQ Manipulation" => FASTQ Quality Trimmer by sliding window". If you are interested, we have recently adapted that tool a bit to improve speed (5'+3' clipping based of 62M reads in about 20 minutes). I can send you the perl script & xml for use in galaxy. Best Regards, Geert Vandeweyer University of Antwerp, Belgium On 11/16/2011 03:44 PM, Soetkin Versteyhe wrote:
Hi all,
Does anyone know if it is possible to trim/clip a sequence from the 5’ end? Thank you.
Best, Soetkin.
*Soetkin Versteyhe, PhD** *PostDoc**
* University of Copenhagen *Faculty of Health Sciences
*The Novo Nordisk Foundation* *Center for Basic Metabolic Research*
Integrative Physiology
Blegdamsvej 3B * *2200 København N
Denmark* ** *PHONE +45 35337116*
*_soetkin.versteyhe@sund.ku.dk__ _http://sund.ku.dk http://metabol.ku.dk <http://metabol.ku.dk/>* **
*
___________________________________________________________ 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:
Hello Soetkin, A tools search using the keyword "trim" will bring up the options in Galaxy, the simplest being the FASTX-toolkit "Trim" function. To enable searching, use the the "Options" menu in the top left tool menu panel. Thanks for using Galaxy! Jen Galaxy team http://galaxyproject.org/wiki/Support On 11/16/11 6:44 AM, Soetkin Versteyhe wrote:
Hi all,
Does anyone know if it is possible to trim/clip a sequence from the 5’ end? Thank you.
Best, Soetkin.
*Soetkin Versteyhe, PhD** *PostDoc**
* University of Copenhagen *Faculty of Health Sciences
*The Novo Nordisk Foundation* *Center for Basic Metabolic Research*
Integrative Physiology
Blegdamsvej 3B * *2200 København N
Denmark* ** *PHONE +45 35337116*
*_soetkin.versteyhe@sund.ku.dk__ _http://sund.ku.dk http://metabol.ku.dk <http://metabol.ku.dk/>* **
*
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
participants (3)
-
Geert Vandeweyer -
Jennifer Jackson -
Soetkin Versteyhe