Question: How do I convert Hisat2 + stringtie gtf to EVM compatible gff3
0
gravatar for karthic
3 months ago by
karthic100
karthic100 wrote:

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 • 227 views
ADD COMMENTlink modified 3 months ago by Juke345.1k • written 3 months ago by karthic100

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

ADD REPLYlink written 3 months ago by asumani70
0
gravatar for Juke34
3 months ago by
Juke345.1k
Sweden
Juke345.1k wrote:

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

ADD COMMENTlink written 3 months ago by Juke345.1k

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 REPLYlink written 3 months ago by karthic100

could you show few lines of the GTF file?

ADD REPLYlink written 3 months ago by Juke345.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1373 users visited in the last hour
_