Clipping From 5' End

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Question: Clipping From 5' End

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7.0 years ago by

Soetkin Versteyhe • 30

Soetkin Versteyhe • 30 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 Křbenhavn 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]

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modified 7.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.0 years ago by Soetkin Versteyhe • 30

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7.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

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7.0 years ago by

Geert Vandeweyer • 40

Geert Vandeweyer • 40 wrote:

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

ADD COMMENT • link written 7.0 years ago by Geert Vandeweyer • 40

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