Converting gff3 to gtf file format?

Question

[melatoninixo]

Hi all, I am trying to convert a gff3 file obtained from ensembl to gtf but to no avail. I have tried to convert my gff3 file to gtf by using gffread which is what most suggested to people facing similar issues on other forums. Although it seemed to have worked for most, the output I got in my working directory was instead an empty gtf file. The command I have used is as below:

gffread 'Saccharomyces_cerevisiae_cen_pk113_7d_gca_000269885.ASM26988v1.52.gff3' -T -o output.gtf

What could have been the problem? Any input is greatly appreciated, thank you!

Answer 1

[Ben_Ensembl]

Hi melatoninixo,

You can also retrieve the S. cerevisiae GTF file directly from the Ensembl Genomes FTP site: http://ftp.ensemblgenomes.org/pub/fungi/release-52/gtf/saccharomyces_cerevisiae/

[melatoninixo]

Thank you for responding. That gtf however belongs to S288C strain but not CEN PK which I am interested in analyzing

[Ben_Ensembl]

No problem. You can find the GTF for the CEN PK strain in the 'fungi_ascomycota1_collection' directory: http://ftp.ensemblgenomes.org/pub/fungi/release-52/gtf/fungi_ascomycota1_collection/saccharomyces_cerevisiae_cen_pk113_7d_gca_000269885/

[melatoninixo]

Wow thank you so much!

[Ben_Ensembl]

No problem

Answer 2

[Juke34]

Conversion info here: https://agat.readthedocs.io/en/latest/gff_to_gtf.html

Try agat_convert_sp_gff2gtf.pl from AGAT

[melatoninixo]

Will try it out, thank you for your input!