fastq quality trimmer

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fastq quality trimmer

Tomaz Rijavec
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 / www.ifb.si
Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana, Slovenia / T: +3861 587 54 70 / www.ifb.si

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Re: fastq quality trimmer

Jen Hillman-Jackson
Hello Tomaž,

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,
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 / www.ifb.si
Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana, Slovenia / T: +3861 587 54 70 / www.ifb.si


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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To search Galaxy mailing lists use the unified search at:

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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: fastq quality trimmer

Dannon Baker-2
In reply to this post by Tomaz Rijavec
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 https://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastq/fastq_trimmer_by_quality.py?at=default

-Dannon



On Wed, Apr 17, 2013 at 7:30 AM, Tomaz Rijavec <[hidden email]> 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 / www.ifb.si
Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana, Slovenia / T: <a href="tel:%2B3861%20587%2054%2070" value="+38615875470" target="_blank">+3861 587 54 70 / www.ifb.si

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/