Question: Downloading hg38 centromere and telomere positions from UCSC table browser
0
gravatar for graeme.thorn
4 months ago by
graeme.thorn50
London, United Kingdom
graeme.thorn50 wrote:

I'm converting an R code (from here: https://github.com/cancer-genomics/delfi_scripts) from hg19 to hg38 assembly, and it relies on automatically downloading telomeric and centromeric regions from the UCSC table browser:

genome <- "hg19"
mySession <- browserSession()
genome(mySession) <- genome
gaps <- getTable(ucscTableQuery(mySession, track="gap"))

in order that the resulting fragment calculations don't cover (some of) the less mappable regions of the genome. However, the corresponding code for hg38:

genome <- "hg38"
mySession <- browserSession()
genome(mySession) <- genome
gaps <- getTable(ucscTableQuery(mySession, track="gap"))

does not return the centromere positions from the UCSC table (it has all the telomeric ranges). I have tested the online table browser and that does not return hg38 centromere positions either. Is there another source for these?

ucsc R genome • 284 views
ADD COMMENTlink modified 1 day ago by ATpoint38k • written 4 months ago by graeme.thorn50

While UCSC support stops by here once in a while you should probably report this directly to them (genome at soe.ucsc.edu) and then provide an update here.

ADD REPLYlink written 4 months ago by genomax89k

I will provide feedback to them about this. However, I'm just looking for a table of positions in hg38 that I can bolt on to the existing removed regions to ease the workflow.

EDIT: it does look like this is a frequent question to them, see for instance here: https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/SaR2y4UNrWg/XsGdMI3AazgJ

The answer to this query doesn't really help, though.

ADD REPLYlink modified 4 months ago • written 4 months ago by graeme.thorn50

Hi, still any solution?

I'm looking for the centromeric regions in release GRCh38.

I would need something like: chr start end

I don't understand where I can find it, I looked everywhere and still there is no direct information.

Thanks

ADD REPLYlink written 1 day ago by Simo30

See my answer.

ADD REPLYlink written 1 day ago by ATpoint38k
0
gravatar for ATpoint
1 day ago by
ATpoint38k
Germany
ATpoint38k wrote:

For centromers, the table browser is the answer.

Select BED as output format, then get output, then whole gene, then get BED, done.

enter image description here

ADD COMMENTlink modified 1 day ago • written 1 day ago by ATpoint38k
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