question about fastq groomer

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question about fastq groomer

kenlee nakasugi
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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Re: question about fastq groomer

Jen Hillman-Jackson
Hello Ken,

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.

usage:
fastq_groomer.py input_file input_type output_file output_type
output_quality_score_encoding summarize_input

where input_type and output_type can each be one of:
sanger
illumina
solexa
cssanger

output_quality_score_encoding can be:
ascii
decimal
None

summarize_input can be:
summarize_input
dont_summarize_input

Hopefully this will get you going, but please let us know if we can help
more,

Thanks,

Jen
Galaxy Team


On 8/16/10 7:22 AM, kenlee nakasugi 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
>
>
>
> _______________________________________________
> galaxy-user mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user

--
Jennifer Jackson
http://usegalaxy.org
_______________________________________________
galaxy-user mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user
Jennifer Hillman-Jackson
http://galaxyproject.org