Hi Jeltje,
Thank you for your question about obtaining centromere coordinates for
hg38. You can get slightly different centromere coordinates than the
centromeres track via the cytoBandIdeo table. Similar to before, head
to the Table Browser and choose the Mapping and Sequencing group,
although instead of selecting the gap track, select the "Chromosome
Band (Ideogram)" track. Then select filter, and enter "*cen*" in the
gieStain field. This leads to output like the following:
#filter: cytoBandIdeo.gieStain like '%cen%'
#chrom chromStart chromEnd name gieStain
chr1 121700000 123400000 p11.1 acen
chr1 123400000 125100000 q11 acen
chr2 91800000 93900000 p11.1 acen
chr2 93900000 96000000 q11.1 acen
Here each chromosome will have two entries, and will overlap so you
can merge them into a single entry. Unfortunately, these coordinates
will differ from those in the centromeres track, even if you were to
create single, per chromosome entries out of the centromeres track
items. You may find this previously answered mailing list question
helpful in deciding what data set to choose:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/SaR2y4UNrWg/XsGdMI3AazgJ
Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to
gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to
genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
On Thu, Jan 26, 2017 at 8:58 AM, Jeltje van Baren
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