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.
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written
by
arsala521 •
1 answer
$ 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
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
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?
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