Fastq Quality Trimmer

Question: Fastq Quality Trimmer

5.6 years ago by

Dear "Galaxy Team", I have a question regarding the fastq quality trimmer (by sliding window) tool. What is the script running behind it? Is it a modified version of the fastx_quality_trimmer found in the fastx tools package? Is there a standalone version of it one can set up locally and run it from the command line. Thanks for all the info you can provide. best regards, Tomaž -- Lep pozdrav / Best Regards, dr. Tomaž Rijavec Inštitut za fizikalno biologijo d.o.o. / Toplarniška ulica 19, 1000 Ljubljana / T: 01 587 54 70 / www.ifb.si Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana, Slovenia / T: +3861 587 54 70 / www.ifb.si

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modified 5.6 years ago by Dannon Baker • 270 • written 5.6 years ago by Tomaz Rijavec • 10

5.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Tomaz(, There are three trimming tools. One is from the FASTX Tool kit, the others are not, and all can be run from the command line. They can be found in the Galaxy distribution: http://getgalaxy.org Tool names that you will see in the web browser mapped to where the wrappers are in the distribution. The xml file is the form displayed, the py file is the actual script. The 2nd one is the tool you asked about and it is not from the FASTX Toolkit. FASTQ Trimmer galaxy-dist / tools / fastq / fastq_trimmer.xml galaxy-dist / tools / fastq / fastq_trimmer.py FASTQ Quality Trimmer ( by sliding window) galaxy-dist / tools / fastq / fastq_trimmer_by_quality.xml galaxy-dist / tools / fastq / fastq_trimmer_by_quality.py Trim sequences galaxy-dist / tools / fastx_toolkit / fastx_trimmer.xml FastXToolkit source: http://hannonlab.cshl.edu/fastx_toolkit/ Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.6 years ago by Jennifer Hillman Jackson ♦ 25k

5.6 years ago by

Dannon Baker • 270

United States

Dannon Baker • 270 wrote:

Hi Tomaž, The script depends on galaxy libraries, but could probably be set up standalone if you made the appropriate libraries available -- the source is distributed with galaxy, see https://bitbucket.org/galaxy/galaxy- central/src/tip/tools/fastq/fastq_trimmer_by_quality.py?at=default -Dannon

ADD COMMENT • link written 5.6 years ago by Dannon Baker • 270

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