Centromere and telomere positions for Chm13v2 assembly

Question

[arsala521]

Hi everyone,

I am looking for centromere and telomere positions for the new human assembly, chm13v2. Are there any files for these positions under https://hgdownload.soe.ucsc.edu/downloads.html#human I tried to dig in but couldn't find.

If there is no file available for chm13 centromere positions, can someone please tell the best approach to identify centromeric regions? I was thinking to select the constricted region on chromosome on ucsc genome browser and further refine/extend the box position until there is end of Ns on both side.

I shall be very grateful for any help/hint.

Answer 1

[Pierre Lindenbaum]

$ wget  "https://hgdownload.soe.ucsc.edu/gbdb/hs1/cytoBandMapped/cytoBandMapped.bb" 
$ bigBedToBed cytoBandMapped.bb stdout | head
chr1    0   1735965 p36.33  gneg
chr1    1735965 4816989 p36.32  gpos25
chr1    4816989 6629068 p36.31  gneg
chr1    6629068 8634052 p36.23  gpos25
chr1    8634052 12044143    p36.22  gneg
chr1    12044143    15341266    p36.21  gpos50
chr1    15341266    19923637    p36.13  gneg
chr1    19923637    23434574    p36.12  gpos25
chr1    23434574    27441306    p36.11  gneg
chr1    27441306    29743244    p35.3   gpos25

[jleehan]

Are the telomeres just the first and last bands on this table for each chromosome? I know "acen" is supposed to represent centromeres, but is there an identifier that specifically represents the telomeres?

[GenoMax]

These are centromere/telomere positions?

[Pierre Lindenbaum]

GenoMax ah yes, you're right, it's not clear here. the old files contained that information : How Can I Get The Human Chromosome Centromere Position And Chromosome Length In Grch37/Hg19

[arsala521]

Thank you. The 5th column of this file shows acen entries as well. I think I can take that as centromere regions. Any idea about any file with telomere positions?