genetic coordinates hg19/GRCh37 latest version

Question

[cocchi.e89]

Dear all,

maybe is a silly question, but I'd like to know if the file: "interim_GRCh37.p13_top_level_2017-01-13.gff3" (ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz) is the latest version to get genetic coordinates (hg19) of some genes.

As example, I found that when compared with UCSC (https://genome.ucsc.edu/cgi-bin/hgTables) the START coordinates is alway 1bp before and same for exams coordinates.

Let me know if you know something more specifically.

Thanks a lot in advance.

Answer 1

[GenoMax]

Yes for the first.Gencode release 19 is the latest release for hg19 (GRCh37.p13): https://www.gencodegenes.org/human/release_19.html

Check out this blog post about co-ordinate systems used by UCSC tools: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/