StringTie to GFF3

Question

[Ric]

Hi, I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

##gff-version 3
NbV1Ch01        StringTie       mRNA    212226  219213  1000.00 -       .       ID=STRG.3.1;geneID=STRG.3
NbV1Ch01        StringTie       exon    212226  212731  1000.00 -       .       Parent=STRG.3.1
NbV1Ch01        StringTie       exon    212829  212968  1000.00 -       .       Parent=STRG.3.1
NbV1Ch01        StringTie       exon    218080  219213  1000.00 -       .       Parent=STRG.3.1
NbV1Ch01        StringTie       mRNA    212226  219213  1000.00 -       .       ID=STRG.3.2;geneID=STRG.3
NbV1Ch01        StringTie       exon    212226  212731  1000.00 -       .       Parent=STRG.3.2
NbV1Ch01        StringTie       exon    212829  212968  1000.00 -       .       Parent=STRG.3.2
NbV1Ch01        StringTie       exon    218080  218969  1000.00 -       .       Parent=STRG.3.2
NbV1Ch01        StringTie       exon    219061  219213  1000.00 -       .       Parent=STRG.3.2

How is it possible to merge all the above two mRNA features (different splice forms) into a gene feature, as shown below?

##gff-version 3
NbV1Ch01        StringTie       gene    212226  219213  1000.00 -       .       ID=STRG.3
NbV1Ch01        StringTie       mRNA    212226  219213  1000.00 -       .       ID=STRG.3.1;Parent=STRG.3
NbV1Ch01        StringTie       exon    212226  212731  1000.00 -       .       Parent=STRG.3.1
NbV1Ch01        StringTie       exon    212829  212968  1000.00 -       .       Parent=STRG.3.1
NbV1Ch01        StringTie       exon    218080  219213  1000.00 -       .       Parent=STRG.3.1
NbV1Ch01        StringTie       mRNA    212226  219213  1000.00 -       .       ID=STRG.3.2;Parent=STRG.3
NbV1Ch01        StringTie       exon    212226  212731  1000.00 -       .       Parent=STRG.3.2
NbV1Ch01        StringTie       exon    212829  212968  1000.00 -       .       Parent=STRG.3.2
NbV1Ch01        StringTie       exon    218080  218969  1000.00 -       .       Parent=STRG.3.2
NbV1Ch01        StringTie       exon    219061  219213  1000.00 -       .       Parent=STRG.3.2

Thank you in advance,

[Mensur Dlakic]

It seems like you need a short script that reads all mRNA lines, picks the smallest start coordinates and largest end coordinates, and writes a line with gene designation. That should doable with few lines of code in a variety of scripting languages.

Answer 1

[Juke34]

Using gxf_to_gff3.pl from the GAAS toolkit you will end up with what you wish for.

gxf_to_gff3.pl -g stringtie.gtf -o stringtie_standardized.gff3