Question: Convert gff format file to circos band table
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gravatar for 2012201024
5.2 years ago by
201220102420
China
201220102420 wrote:

Hi,

I have a genes.annotation.gff file, such as:

chrC09 GazeA2 mRNA 9318184 9322857 214.6819 - . ID=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001
chrC09 GazeA2 CDS 9322739 9322857 23.0574 - 0 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001
chrC09 GazeA2 CDS 9322374 9322646 15.0804 - 2 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001
chrC09 GazeA2 UTR 9318184 9318353 1.5570 - . Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001
chrC09 GazeA2 mRNA 9310901 9313544 288.8598 + . ID=BnaC09g12810D;Name=BnaC09g12810D;Alias=GSBRNA2T00000003001

I want to convert this file to a band table in circos format, which has no copy region and has color code. (In fact, I  guess if the bank line represents the gene density in limited region?)

Many thanks in advance!

 

 

ciros • 2.2k views
ADD COMMENTlink modified 5.2 years ago by Alex Reynolds29k • written 5.2 years ago by 201220102420
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gravatar for Alex Reynolds
5.2 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

If you want to make a tile rendering, you could read the sample configuration to get a demonstration of how it is done. Then you would write a script with awk or another language to convert fields in your GFF file to a minimally three-column text file (or four, if you want to add a text label).

ADD COMMENTlink written 5.2 years ago by Alex Reynolds29k
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