Question: extracting the exons coordinates on hg38
0
gravatar for Bogdan
17 months ago by
Bogdan720
Palo Alto, CA, USA
Bogdan720 wrote:

Dear all,

please could you advise : how can we obtain the coordinates of exons of the RefSeq or UCSC genes (canonical isoforms) on hg38, where each coordinates (chr, start, end) also have assigned the gene name .. ?

thanks a lot, and a happy weekend,

-- bogdan

exome genome • 1.2k views
ADD COMMENTlink modified 17 months ago by chen1.8k • written 17 months ago by Bogdan720

Hello Bogdan!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/101333/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 17 months ago by WouterDeCoster37k

Dear gentlemen, thank you for your replies : very much appreciate your help ;). Yes, i knew the previous postings related to extracting the hg19 exon coordinates before i emailed ; although it applies a bit differently to hg38 and to RefSeq genes.

I thought that we may find 2 solutions to the same question : in BioC (by using GenomeFeatures), and in a not-BioC related manner; that I can compare afterwards.

thanks again for your hep, and happy weekend ;) !

ADD REPLYlink modified 17 months ago • written 17 months ago by Bogdan720
0
gravatar for chen
17 months ago by
chen1.8k
OpenGene
chen1.8k wrote:

Try OpenGene.jl, a library written in Julia (https://github.com/OpenGene/OpenGene.jl).

using OpenGene, OpenGene.Reference

# load the gencode dataset, it will download a file from gencode website if it's not downloaded before
# once it's loaded, it will be cached so future loads will be fast
index = gencode_load("GRCh38")

genes = gencode_genes(index, "TP53")
tp53 = genes[1]
exons = tp53.transcripts[1].exons
#print the exons
for exon in exons:
    println(exon.number, exon.start_pos, exon.end_pos)
end
ADD COMMENTlink modified 17 months ago • written 17 months ago by chen1.8k
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