Question: Fastq Quality Trimmer
gravatar for Tomaz Rijavec
5.6 years ago by
Tomaz Rijavec10 wrote:
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 / Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana, Slovenia / T: +3861 587 54 70 /
galaxy • 3.4k views
ADD COMMENTlink modified 5.6 years ago by Dannon Baker270 • written 5.6 years ago by Tomaz Rijavec10
gravatar for Jennifer Hillman Jackson
5.6 years ago by
United States
Jennifer Hillman Jackson25k 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: 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 Quality Trimmer ( by sliding window) galaxy-dist / tools / fastq / fastq_trimmer_by_quality.xml galaxy-dist / tools / fastq / Trim sequences galaxy-dist / tools / fastx_toolkit / fastx_trimmer.xml FastXToolkit source: Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training
ADD COMMENTlink written 5.6 years ago by Jennifer Hillman Jackson25k
gravatar for Dannon Baker
5.6 years ago by
Dannon Baker270
United States
Dannon Baker270 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 central/src/tip/tools/fastq/ -Dannon
ADD COMMENTlink written 5.6 years ago by Dannon Baker270
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