Re: [genome] Requesting a bed file format of Gallus_gallus7b for a recent version of ensembl

[Luis Nassar]

Hello, Suelen.

You are correct that the file was built from a previous version, however, not all annotations change on each Ensembl version update. Sometimes none do. You could verify the items with the latest release to compare, or alternatively, you could regenerate the files yourself.

You can download the latest ensemble GTF file and create a bed using a combination of two of our utilities (
https://hgdownload.soe.ucsc.edu/downloads.html?#utilities_downloads). You will need to use gtfToGenePred and then genePredToBed. You can see an example of a similar workflow on the following page:

https://genome.ucsc.edu/goldenPath/help/bigGenePred.html

You would just use genePredToBed instead of genePredToBigGenePred at the end.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

On Mon, Jul 1, 2024 at 3:32 PM Suelen Fernandes Padilha <suelenf...@gmail.com> wrote:

Dear Team,

The version of the BED file available on the website for Gallus_gallus7b is from an old version of ensembl, I believe it is version 109 as the website was last updated in May 2023.

Is there an updated version of the BED file for Gallus7b in ensembl 112? because I tried to transform from a GTF and GFF file and was unsuccessful for my analyzes in the R software with the genometion package. It seems that the package requires some coordinates of introns, promoter regions, etc., which when converted from a GTF/GFF file do not exist.

Thanks and regards,

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[Suelen Fernandes Padilha]

Hello,

Thank you for the information.

Regargs, 

Suelen Fernandes Padilha Aleixo
Doutoranda em Zootecnia
Universidade Federal do Paraná - UFPR