hg38 annotation file (gtf) UCSC format

Question

[dina.hesham139]

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!

Answer 1

[inambioinfo]

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.

Answer 2

[trausch]

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

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

[dina.hesham139]

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

[Devon Ryan]

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

[anu014]

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

[khorms]

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

[amina.mcdiarmid]

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