Question About Plotting Circos Plot

Question: Question About Plotting Circos Plot

6.7 years ago by

United States

shamsher jagat • 590 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

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modified 6.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.7 years ago by shamsher jagat • 590

6.7 years ago by

shamsher jagat • 590

United States

shamsher jagat • 590 wrote:

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

ADD COMMENT • link written 6.7 years ago by shamsher jagat • 590

6.7 years ago by

Björn Grüning • 350

Björn Grüning • 350 wrote:

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 -- 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/

ADD COMMENT • link written 6.7 years ago by Björn Grüning • 350

6.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

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