CHM13 cytoband positions for building an ideogram

Question

CHM13 cytoband positions for building an ideogram

mike-molnar opened this issue 2 years ago · 4 comments

Hello,

Thanks for all your great work in building the CHM13 assembly! I would like to plot some of my results of v2.0 using karyoploteR, and I am able to build a custom ideogram, but I cannot find a file with the positions of the cytobands. I see the centromere and telomere files for v1.1 on the UCSC table browser, but I was wondering if there is a BED file with all of the cytoband positions?

Thanks,
Mike

Answer 1 · 2022-03-02T18:21:25.000Z

Hi Mike, I put the V2.0 cytoband BED here: http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v2.0/download/chm13v2.0_cytobands_allchrs.bed.gz Mark

Answer 2 · 2022-03-02T18:38:22.000Z

Hi Mark,

Awesome! Thanks for the quick reply.

Mike

Answer 3 · 2022-09-05T07:41:03.000Z

Hi Mike, I put the V2.0 cytoband BED here: http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v2.0/download/chm13v2.0_cytobands_allchrs.bed.gz Mark

Hi Diekhans,

The link is broken, can you provide it again?

Thanks a lot !
Huihui Li

Answer 4 · 2022-09-05T17:58:07.000Z

Apologies, the link broke as part of reorganizing around moving to UCSC. This link should work again: http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v2.0/download/chm13v2.0_cytobands_allchrs.bed.gz