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 <greg@bx.psu.edu> *To:* Alejandra Rougon <alerougon@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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support