Question

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

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3.5 years ago

karthic ▴ 130

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 • 2.3k views

ADD COMMENT • link updated 2.1 years ago by giacuong171 ▴ 10 • written 3.5 years ago by karthic ▴ 130

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

ADD REPLY • link 3.5 years ago by asumani ▴ 70

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

ADD REPLY • link 2.7 years ago by memy ▴ 20

score 1 · Answer 1 · 2022-03-05

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2.1 years ago

giacuong171 ▴ 10

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

ADD COMMENT • link 2.1 years ago by giacuong171 ▴ 10

score 0 · Answer 2 · 2020-11-05

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3.5 years ago

Juke34 8.5k

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

ADD COMMENT • link 3.5 years ago by Juke34 8.5k

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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.

ADD REPLY • link 3.5 years ago by karthic ▴ 130

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could you show few lines of the GTF file?

ADD REPLY • link 3.5 years ago by Juke34 8.5k