Centromere hg38

Question

[heureuse]

Good morning, I need centromere file of hg38. The one I download from ucsc is chunked with 110 lines instead of 24 lines. I wrote a script to merge them but if I take the positions and put them on ucsc genome browser it only falls on part of the centromere. I think then that I must have downloaded the wrong file.

Do you have an idea on where I can find the good file.

Thank you.

[Pierre Lindenbaum]

I download from ucsc is chunked with 110 lines instead of 24 lines.

which file ? cytoband ? as the filename says, those are the coordinates of the cytogenetics band.

wrote a script to merge them

what have you done ?

see also: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In Grch37/Hg19

[heureuse]

This one.

For the script, for chr1 for example, if I have 3 rows, I will just take the smallest start and the greatest stop. That way I will have just one entry for chr1

[barslmn]

You can use bedtools merge.

wget -q -O- https://genome.ucsc.edu/cgi-bin/hgTables\?hgsid\=1654900614_2cotpic8SktMadZRcx7tYZBbq6md\&boolshad.hgta_printCustomTrackHeaders\=0\&hgta_ctName\=tb_centromeres\&hgta_ctDesc\=table+browser+query+on+centromeres\&hgta_ctVis\=pack\&hgta_ctUrl\=\&fbQual\=whole\&fbUpBases\=200\&fbDownBases\=200\&hgta_doGetBed\=get+BED | 
sort -k1,1V -k2,2n | 
bedtools merge -d 1000000

[heureuse]

thanks a lot