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!
2 answers
You can find the original GTF's for hg38 here: https://www.gencodegenes.org/human/release_20.html
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/
Please check in the parent directory-
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
OR from Ensembl
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/
Log in to answer this question.
-
gtf files for various organism in ucsc
written by 1769mkc
-
zero counts for all genes in RNAseq data of Ferret
written by Sara
-
Forum: How should reference genome fasta files be distributed by UCSC?
written by Maximilian Haeussler
-
What is the different bewteen ucsc simple repeat and tandem repeat
written by octpus616 •
-
STAR Genome index could not open genomeFastaFile
written by bs58 •
-
bedGraphToBigWig error : Expecting at least 3 words line 1 of chrom.sizes. got 2
written by pt.taklifi
-
What's the difference of reciprocal-best netted chains and all chains
written by yunzhe.jiang97 •
-
which gtf file I can use?
written by yueli7
-
Download latest reference genome assembly for exome sequencing alignment and variant calling
written by svlachavas
-
How to align 100 samples with BWA?
written by madkitty
