How do I convert Hisat2 + stringtie gtf to EVM compatible gff3

Question

[karthic]

Hi,

I aligned my rnaseq to the genome using hisat2 and obtained gtf file using stringtie. Now how do i convert this gtf to EVM compatible gff3. I have checked the misc folder in the EVM software, there is no script for this.

Anyone please help

Karthic

[asumani]

You may want to check out 'The gffread utility' header here: http://ccb.jhu.edu/software/stringtie/gff.shtml

[Sadik Muzemil]

how did you solve formatting stringtie gtf to EVM compatible gff3?

Answer 1

[giacuong171]

Hi, you can use cufflinks_gtf_to_alignment_gff3.pl from EVM to convert stringtie.gtf to gff3 format.

Answer 2

[Juke34]

You can try AGAT with agat_convert_sp_gxf2gxf.pl I use it often with Stringtie output to get standardized gff3 files.

[karthic]

Thanks Juke. Still EVM throws the following error

Fatal Error, cannot locate data entry for ID: [STRG.26026.1] at gff3_gene_prediction_file_validator.pl line 125

I just converted the gtf to gff3 with the following command

agat_convert_sp_gxf2gxf.pl -g stringtie.gtf -o stringtie.gff3

Karthic.

[Juke34]

could you show few lines of the GTF file?