Convert gff format file to circos band table

Question

[2012201024]

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!

Answer 1

[Alex Reynolds]

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).