GTF annotation file for Hg38 Dec 2013 (First Release)

Question

[Daniel]

Hello,

I am looking for the GTF file corresponding to the initial Dec. 2013 hg38 release. I have tried looking including here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/ but the directory does not contain the file (it does contain the original .fa file, though). I need both files to use for multiz's 100-way vertebrate alignment files.

Thanks!

Answer 1

[GenoMax]

You can find the original GTF's for hg38 here: https://www.gencodegenes.org/human/release_20.html

[Daniel]

Thanks but I believe I need the first version which is UCSC's? I think Gencode's release 20 was modified in 2014 to be the first hg38 gencode release.

[GenoMax]

GRC is the main organization responsible for genome builds of model organisms (NCBI, UCSC, Ensembl all provide additional derivative annotation).

So if you prefer get the original release from their page https://www.ncbi.nlm.nih.gov/grc/human

Actual link for the FTP site is: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/

Answer 2

[bk11]

Please check in the parent directory-

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

OR from Ensembl

https://useast.ensembl.org/info/data/ftp/index.html

[Daniel]

Unfortunately it doesn't appear to be there :(

I'm worried about downloading from Ensembl because I need the gtf file to be compatible with UCSC's multiz 100-way alignment.

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/