galaxy use of Circos for chromatin interaction data

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Mauricio Barajas

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May 17, 2021, 3:54:00 PMMay 17
to Circos
Hi everyone

I've been trying to use Circos (using Galaxy) for plotting chromatin interaction in a specific part of the genome. I tried using this type of data:
chr1 start1 end1 chr2 start2 end2
chr6 69400000 69450000 chr6 69900000 69950000 
chr6 69400000 69450000 chr6 70000000 70050000
chr6 69450000 69500000 chr6 69850000 69900000

I get an error like this:
"slice indices must be integers or None or have an __index__ method"

Any idea what is the problem? 

Also, when I change the parameters to show chr6 instead of my area of interest (~2MB), I get a plot but it is empty.

Thanks,

Mauricio B.


Martin

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May 17, 2021, 3:57:07 PMMay 17
to Circos
Human chromosomes are indexed by prefix "hs" not "chr". You'll need to change your inputs to

hs6 69400000 69450000 hs6 ...
...

For more details see my Galaxy training workshop slides

Mauricio Barajas

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May 20, 2021, 3:32:35 PMMay 20
to circos-data-...@googlegroups.com
Thanks! It worked

Mauricio

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