Question: Question About Fastq Groomer
0
kenlee nakasugi • 60 wrote:
Hi All,
I'm new to NGS analysis, and command line analysis for that matter.
(I'm in the process of learning perl/python - so please bear with this
newbie query).
I've installed the fastx-toolkit and the scripts here are working
great, but couldn't find the fastq_groomer script anywhere on the
galaxy page, at http://hannonlab.cshl.edu/fastx_toolkit/index.html,
nor on the web, except from this page: http://bitbucket.org/galaxy
/galaxy-dist/src/tip/tools/fastq/
I tried running it via: python fastq_groomer.py input_file input_type
output_type
as per the fastq_groomer.xml, but doesn't work.
Is this the correct fastq_groomer script, am I running it correctly,
or where can I get this script to run like the other fastx-toolkit
scripts?
I know I could use the Galaxy server/ or install galaxy locally, but
for several reasons at the moment want to use the individual scripts.
Thanks in advance!
Ken
Kenlee Nakasugi
School of Molecular Bioscience
University of Sydney
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modified 8.3 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
8.3 years ago by
kenlee nakasugi • 60
