Question: Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Files?
3
gravatar for Shaojiang Cai
5.7 years ago by
Shaojiang Cai100
Singapore
Shaojiang Cai100 wrote:

Hi, I am hanging around to look for hg19 transcript annotations together with cDNA fasta files.

From UCSC, I can download the gene annotation, but without transcripts. I know that I can infer from the genome once I get the transcript annotation, but is there any place where I can download the transcript annotation and cDNA Fasta files?

I also would like to know the correspondence between the genes and transcripts. Say, transcripts A, B and C are from gene G.

Thanks.

hg19 ucsc • 20k views
ADD COMMENTlink modified 3.8 years ago by aebmad20 • written 5.7 years ago by Shaojiang Cai100
3
gravatar for Nicolas Rosewick
5.7 years ago by
Belgium, Brussels
Nicolas Rosewick7.4k wrote:

everything is available here : http://www.ensembl.org/info/data/ftp/index.html

ADD COMMENTlink written 5.7 years ago by Nicolas Rosewick7.4k
1
gravatar for aebmad
3.8 years ago by
aebmad20
United States
aebmad20 wrote:

For the transcript annotation file, I use the genePredToGtf script from UCSC which allows you to create a GTF annotation file. You can find a detailed explanation of how to download and use the script here: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format

Alex

ADD COMMENTlink written 3.8 years ago by aebmad20

Just to clarify in case anyone in the future uses genePredToGtf, in the 2nd step the section "region should be set to "position" instead of genome" should only be followed for the example and not for the actual GTF derivation. Leave it as "genome" when actually deriving a GTF file in this manner.

ADD REPLYlink written 15 months ago by pjmaguire370
0
gravatar for sgujja
4.6 years ago by
sgujja20
United States
sgujja20 wrote:

Hi,

I came across your post while looking to download hg19 Transcript Annotation file with correspondence between transcripts and gene.

Could you please let me know where you were able to download it from.

Thanks

Sharvari

ADD COMMENTlink written 4.6 years ago by sgujja20
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