How do I convert Hisat2 + stringtie gtf to EVM compatible gff3
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10 months ago
karthic ▴ 110

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

RNA-Seq gene prediction • 596 views
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You may want to check out 'The gffread utility' header here: http://ccb.jhu.edu/software/stringtie/gff.shtml

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

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10 months ago
Juke34 ★ 6.3k

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

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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.

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could you show few lines of the GTF file?

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