Portions of the Galaxy distribution from bitbucket are required to run
fastq_groomer.py on the command line. Specifically, obtain the source
and then add galaxy/lib to your PYTHONPATH.
fastq_groomer.py input_file input_type output_file output_type
where input_type and output_type can each be one of:
output_quality_score_encoding can be:
summarize_input can be:
Hopefully this will get you going, but please let us know if we can help
On 8/16/10 7:22 AM, kenlee nakasugi wrote:
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
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,
, nor on the web,
except from this page:
I tried running it via: python fastq_groomer.py input_file input_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!
School of Molecular Bioscience
University of Sydney
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