I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881 Any suggestion for an alternative tool will also be appreciated. Thanks Shamsher
My apology for re-posting the same question however I believe my first message was returned. I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881 Any suggestion for an alternative tool will also be appreciated. Thanks Shamsher
Hi Shamsher. We have a small initial wrapper for circos. Its not complete yet and we are not sure if its even possible to wrap such a complex tool in a good galaxy UI. But if you are interested i can share our code. Cheers, Bjoern
I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881
Any suggestion for an alternative tool will also be appreciated.
Thanks
Shamsher ___________________________________________________________ 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:
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-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
Hello Shamsher, Another user posted that they have started a Galaxy wrapper for the Circos tool itself, but I wanted to let you know about the tool "EMBOSS -> cirdna: Draws circular maps of DNA constructs". The link on the tool's form points to all of the EMBOSS tools, including this specific page for the cirdna tool: http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/cirdna.html The version in Galaxy is 5.0.0 and is a simplified implementation compared to the command-line. The tool form accepts a dataset from the history as input and uses default options. Please see the cirdna.html documentation for instructions about how to format the input file (created outside of Galaxy and uploaded as a text file). There is an example in the documentation if you want to get an idea about what the resulting graphic will look like as implemented in Galaxy (versus the graphic in the documentation). Best, Jen Galaxy team On 3/6/12 8:32 PM, shamsher jagat wrote:
I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881 Any suggestion for an alternative tool will also be appreciated. Thanks Shamsher
___________________________________________________________ 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:
participants (3)
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Björn Grüning -
Jennifer Jackson -
shamsher jagat