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eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Support T2T human genome #314

Open LuisGFdez opened 2 years ago

LuisGFdez commented 2 years ago

I have certain coordinates that I would like to map in T2T, but from what I know is that it is still not available a version in ideogram for T2T

eweitz commented 2 years ago

This seems worthwhile indeed. Do you know where I can find coordinates for T2T centromeres?

LuisGFdez commented 2 years ago

This is the file with all the pericentromeric and centromeic regions of T2T http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1470519897_5lu8DAAPH6GRG7R5iKraehYaOhya&db=hub_3671779_hs1&c=chr9&g=hub_3671779_censat

As it is fully solved T2T, there is not a file that only have the centromeric regions. In this file it is inlcued all the satellite rich regions

You can donwload it from here: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1470519505_tISw18NHo3kN6AKrZp5GOW1A9tGL&clade=hub_3671779&org=hub_3671779_Human&db=hub_3671779_hs1&hgta_group=map&hgta_track=hub_3671779_censat&hgta_table=0&hgta_regionType=range&position=chr9%3A145%2C458%2C455-145%2C495%2C201&hgta_outputType=selectedFields&hgta_outFileName=