Hi Scott,

There isn't a pre-made tool to do this, but creating a workflow to do some counts is possible.


Using a combination of tools in "Text Manipulation" ('Cut'), "Join, Subtract and Group" ('Group'), and/or maybe "Statistics" ('Count'), should allow you to work with a simplified tabular file of hits to identify the query sequences with low specificity, then filter the associated alignments out of the primary data ('Join' or 'Compare two Datasets').

There are probably several ways to do this, but the general idea would be to cut out the query and hit IDs, perform some counts, then filter to only keep the query IDs that meet your criteria. Then, use that list to pull out the associated alignments from the original set (SAM or Interval or other text based format).

If your data are very large, you might need to split this up into a few working files (being sure to keep all of the alignments for a particular query in the same analysis group).

Hopefully this helps,

Best,

Jen
Galaxy team

On 2/28/12 3:28 PM, Scott Tighe wrote:
Dear Galaxy

for genome wide metagenomics, I wonder if there is a way to purge
conserved sequences. For example, if I have 99% of 10 million reads have
perfect alignment to more then 20 reference sequences, I want them to go
away. Inotherwords I only want unique sequences that align to only a few
reference sequences. As for 16sDNA, a 100bp fragment taken from between
V5 and V6 will align to everything!!! I want to purge that away

Sincerely

Scott

Scott Tighe
Advanced Genome Technology Lab
Vermont Cancer Center at the University of Vermont
149 Beaumont Avenue
Health Science Research Bd RM 305
Burlington Vermont USA 05405
lab  802-656-AGTC (2482)
cell 802-999-6666


On 2/28/2012 6:19 PM, Jennifer Jackson wrote:
Hi,

You will want to assign yourself as an administrator in the
universe_wsgi.ini file.

# Administrative users - set this to a comma-separated list of valid
Galaxy
# users (email addresses). These users will have access to the Admin
section
# of the server, and will have access to create users, groups, roles,
# libraries, and more. For more information, see:
# http://wiki.g2.bx.psu.edu/Admin/Interface
#admin_users = None
^^ uncomment and add your login email here

Other wikis that may be helpful, especially if user login is not yet
set up:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
http://wiki.g2.bx.psu.edu/Admin/Config

Hopefully this helps,

Jen
Galaxy team

On 2/28/12 2:59 PM, Alejandra Rougon wrote:

Thank you Greg, I saw the wiki but I do not see the admin link in my
galaxy interface. How do you open galaxy as an administrator?
t
------------------------------------------------------------------------
*From:* Greg Von Kuster <g...@bx.psu.edu>
*To:* Alejandra Rougon <alerou...@yahoo.com>
*Cc:* "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
*Sent:* Tuesday, 28 February 2012, 14:02
*Subject:* Re: [galaxy-user] Speed up uploading into local Galaxy,
terribly slow!!

You can upload your large file to Galaxy data libraries using a
combination of "Upload files from filesystem paths" and "Do not copy
data into Galaxy's default file store".

See this wiki:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files


For all of the information on Galaxy data libraries, see this wiki:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries

Greg Von Kuster


On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote:

Hello, I tried to search in the forums and although this question has
appeared many times I still don't have a solution.

I cannot manage to upload big files into the local galaxy, it just
takes ages. Can I not just copy and paste into a local directory? why
do I have to upload the files if it is already installed locally?
I do not have a server webpage in order to use the url address option
If I do it through ftp (locally) what ftp address shall I put? ftp
localhost:8080??

Is there any other option to speed up uploading, is so slow that is no
longer worth using it, please help me!

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org <http://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/





___________________________________________________________
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/



___________________________________________________________
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/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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/

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