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
On 4/17/13 4:30 AM, Tomaz Rijavec 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,
Tomaz(
--
Lep pozdrav / Best Regards,
dr. Tomaz( Rijavec
--------------------------------------------------------
Ins(titut za fizikalno biologijo d.o.o. / Toplarnis(ka ulica 19, 1000
Ljubljana / T: 01 587 54 70 / www.ifb.si <http://www.ifb.si>
Institute of Physical Biology / Toplarnis(ka ulica 19, SI-1000
Ljubljana, Slovenia / T: +3861 587 54 70 / www.ifb.si <http://www.ifb.si>
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