Question: hg38 annotation file (gtf) UCSC format
1
gravatar for dina.hesham139
4.7 years ago by
Egypt
dina.hesham139120 wrote:

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 • 24k views
ADD COMMENTlink modified 3.7 years ago by inambioinfo110 • written 4.7 years ago by dina.hesham139120
11
gravatar for inambioinfo
3.7 years ago by
inambioinfo110
inambioinfo110 wrote:

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 COMMENTlink written 3.7 years ago by inambioinfo110
2
gravatar for trausch
4.7 years ago by
trausch1.5k
Germany
trausch1.5k wrote:

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

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

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by trausch1.5k
1

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

ADD REPLYlink written 4.7 years ago by dina.hesham139120

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

ADD REPLYlink written 4.7 years ago by Devon Ryan97k

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

ADD REPLYlink written 4.3 years ago by anu014180

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

ADD REPLYlink written 3.7 years ago by khorms140

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

ADD REPLYlink written 2.7 years ago by amina.mcdiarmid0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1010 users visited in the last hour