Converting gtf file from Ensembl to the UCSC Ensembl format (ensGene.txt format)

Question

[rahu]

Hello,

I'm using a pipeline that requires UCSC annotation downloaded from:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz

I believe this is the format of the ensGene file:

https://genome.ucsc.edu/cgi-bin/hgTables?db=danRer10&hgta_group=genes&hgta_track=ensGene&hgta_table=ensGene&hgta_doSchema=describe+table+schema

UCSC does not have a recently updated gene annotation file for the organism I'm working with, That's why I don't want to download it from the link above. Instead, I want to use the annoation file (gtf) from Ensembl's website. However, it doesn't work with the pipeline I'm using. The pipeline requires the annotation file to be in the format as the ensGene file downloaded from UCSC, which areEnsembl gene predictions but in a different format.

I wonder if there is a way to convert a gtf file derived from Ensembl website to the ensGene format UCSC uses for Ensembl genes?

Answer 1

[sam]

Hi,

Check if AGAT (https://github.com/NBISweden/AGAT) can be used to resolve your issue.

Good Luck!