I used h18/build36, but of course you should use h19/build37 for your probem
How can I get the Human chromosome centromere position and chromosome length In Grch37/Hg19?
This site used to give a good answer, but it does not work now. I can not find ChrN_gap under the positional tables drop box.
Does anyone know how to get centromere position in Table Browser?
7 answers
The positions of the cytobands are available in : http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz" | gunzip -c | grep acen | head
chr1 121100000 124300000 p11.1 acen
chr1 124300000 128000000 q11 acen
chr10 38800000 40300000 p11.1 acen
chr10 40300000 42100000 q11.1 acen
chr11 51400000 52900000 p11.11 acen
chr11 52900000 56400000 q11 acen
chr12 33200000 35400000 p11.1 acen
chr12 35400000 36500000 q11 acen
chr13 13500000 16000000 p11.1 acen
chr13 16000000 18400000 q11 acen
Wow! Thank you very much!
http://genome.ucsc.edu/cgi-bin/hgTables
Just choose All Tables -> table:gap
Centromeres are treated as a gap "type"
#bin chrom chromStart chromEnd ix n size type bridge
23 chr1 121535434 124535434 1270 N 3000000 centromere no
Chromosome length can be accessed from chromInfo
#chrom size fileName
chr1 249250621 /gbdb/hg19/hg19.2bit
chr2 243199373 /gbdb/hg19/hg19.2bit
chr3 198022430 /gbdb/hg19/hg19.2bit
chr4 191154276 /gbdb/hg19/hg19.2bit
chr5 180915260 /gbdb/hg19/hg19.2bit
chr6 171115067 /gbdb/hg19/hg19.2bit
http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks20
Question:
"How do I find the positions of the centromeres and telomeres in a particular assembly?"
Response:
This information can be found in the "gap" database table. Use the Table Browser to extract it. To do this, select your assembly and the gap table, then click the "filter Create" button. Set the "type" field to centromere telomere (separated by a space). For help using the Table Browser, visit the User's Guide.
I am also looking for this, and I find all what we need are included in package GWASTools https://www.rdocumentation.org/packages/GWASTools/versions/1.18.0/topics/centromeres
I have tried
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/dm3/database/cytoBand.txt.gz" | gunzip -c | grep acen | head
, but it didn't show any results.I also tried
http://genome.ucsc.edu/cgi-bin/hgTables
just choose All Tables -> table:gap
Centromeres are treated as a gap "type". The result is different from human genome, the type of the reads are contig not centromere.
#bin chrom chromStart chromEnd ix n size type bridge
594 chr4 1221288 1221388 138 N 100 contig yes
587 chrU 325170 325270 141 N 100 contig yes
588 chrU 429354 442354 143 N 13000 contig yes
589 chrU 543815 543915 145 N 100 contig yes
589 chrU 639309 639409 147 N 100 contig yes
Lastly I tried the third method, it showed the message as follows:
#filter: (gap.type = 'telomere' OR gap.type = 'centromere')
#bin chrom chromStart chromEnd ix n size type bridge
# No results passing filter.
I face to one problem that I can not resolve it. I have a problem for drawing idiogram in sheep chromosomes (I analysis with software: http://visualization.ritchielab.psu.edu/phenograms/plot) because I must have sheep Centromeres Position and chr size in this graph but I can't find information about it.
This question has nothing to do with original subject of this thread. If you want to get an answer then post it as a new question/post. Then come back and delete your post here.
You can pre-process this file http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz and extract the centromeric regions for hg19/GRCh37.
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