hg38 annotation file (gtf) UCSC format
2
2
Entering edit mode
8.5 years ago

Hey,

Does anyone know how to get the annotation gtf file for hg38 assembly UCSC format?

I looked for it but I only found the ensembl one!

RNA-Seq alignment • 39k views
ADD COMMENT
11
Entering edit mode
7.5 years ago
inambioinfo ▴ 110

My answer may be very late, But still it will be usefull for someone who are in need.

UCSC Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables

If Human then

Clade : Mammal

Genome : Human

Assembly : latest one (Currently GRCh38/hg38)

Group : Genes and Gene Predictions

Track : RefSeq Gene

Table : refGene

region : Check genome

Output fromat : GTF - gene transfer format

Output file : hg_ucsc.gtf

Hit on get output

Hope this detail will give you clear idea of how to get the files. But yeah if you want to extract the sequence based on the GTF, I could suggest you to use RefSeq.fasta or cDNA.fasta so that you can able to co-relate the files based on your GTF.

Hope this Helps.

ADD COMMENT
2
Entering edit mode
8.5 years ago
trausch ★ 1.9k

UCSC Table Browser, select your desired annotation table and output format GTF:

http://genome.ucsc.edu/cgi-bin/hgTables

ADD COMMENT
1
Entering edit mode

which track should I choose, the default is GENCODE v22?

ADD REPLY
0
Entering edit mode

UCSC uses Gencode for annotations now, so that should work.

ADD REPLY
0
Entering edit mode

But that GENCODEv4 is just 34Mb as compared to ensmbl one (1.4Gb) . Is something missing in UCSC gtfs?

ADD REPLY
0
Entering edit mode

Also, the Gencode website contains the more recent annotations (v25 at the moment)

ADD REPLY
0
Entering edit mode

Hi! I want to ask a question about this... So there is no separate annotation from UCSC anymore?

ADD REPLY

Login before adding your answer.

Traffic: 2614 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6