I’m using circos to create a visual representation of genomic data, but I’m unable to create cytogenic bands that show up on the image. I’ve managed to create the basic ideogram used by: https://training.galaxyproject.org/training-material/topics/visualisation/tutorials/circos/tutorial.html to depict a cancer genome but I can’t seem to decipher how the band data is stored in ‘hg18_karyotype_bands.tsv’, more specifically how the seventh column is used to generate bands. I’d appreciate any help. Thank you.
Hi @Vignesh_P, I think I can provide some help here. The 7th column is just a named color that you want to use for that band. There are a number of colors built in, here the staining colours are used.
band chr1 p36.33 p36.33 0 2300000 gneg band chr1 p36.32 p36.32 2300000 5300000 gpos25 band chr1 p36.31 p36.31 5300000 7100000 gneg band chr1 p36.23 p36.23 7100000 9200000 gpos25 band chr1 p36.22 p36.22 9200000 12600000 gneg
you can read more about the karyotype table format on their website http://circos.ca/documentation/tutorials/ideograms/karyotypes/lesson