Question: Create Circos Builder
0
gravatar for sarbast.ihsan
3 months ago by
United Kingdom
sarbast.ihsan0 wrote:

Dear all,

Does anyone used Circos builder via usegalaxy.?. I do not know how to get the Cytogenetic Bands and how it looks like?

kind regards, Mustafa

ADD COMMENTlink modified 3 months ago • written 3 months ago by sarbast.ihsan0
2
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Galaxy wrapped version of the Circos tool: Graph/Display Data > Circos Builder creates circos plots from standard bioinformatics datatypes

Help for the underlying Circos tool is here (also linked from the Galaxy tool form): http://circos.ca/documentation/

Specifically, see this section. The UCSC Table browser can be queried directly from within Galaxy with the tool Get Data > UCSC Main or obtain the data from the UCSC Downloads area at http://genome.ucsc.edu and upload it to Galaxy (use FTP for any data over 2 GB in size https://galaxyproject.org/support/loading-data/).

CREATING YOUR OWN IMAGE The first thing you will need is the karyotype for your genome. The karyotype defines the chromosomes (name, size, color) and, optionally, the cytogenetic band pattern. You can obtain karyotypes for many genomes from the cytoBandIdeo table (UCSC genome browser).

You can download the karyotype from the table browser or directly for human hg19 (Feb 2009) hg18 (Mar 2006), mouse mm9 (Jul 2009) mm8 (Mar 2006), rat rn4 (Nov 2004) rn3 (Jun 2003), or other species.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k

Dear Jen,

Many thanks for your answer. However, I have tried to download Cytogenetic bands of Ovis aries and uploaded on the UseGalaxy, but it did not work. I am not sure what the file of cytogenetic bands looks like; I mean which type of format is OK. ?

kind regards, Sarbast

ADD REPLYlink written 3 months ago by sarbast.ihsan0

Hello, Example input is in the test history included with this ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/105

There is an issue with some functions. Updates will post to the ticket.

ADD REPLYlink written 19 days ago by Jennifer Hillman Jackson25k
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