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SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

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jinfang

Junior Member

Join Date: Jul 2019

Posts: 1
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#1

gff2gbSmall

08-14-2019, 12:08 PM

Hi, everyone.
I am in trouble converting gff format file to genbank format.

The gff format file looks like:
Scaffold_15;HRSCAF=18| StringTie| transcript| 1| 558|1000| .| .| gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "11.043011"; FPKM "0.745167"; TPM "1.132539";
Scaffold_15;HRSCAF=18| StringTie| exon| 1| 558|1000| .| .| gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "11.043011";

which is generated by StringTie.

The command is
gff2gbSmallDNA.pl stringtie.gff gene.fasta stringtie.gb

However, I got nothing in stringtie.gb.

Anyone guys who know why I got an empty file.

Thanks.
Tags: augustus, genbank, gff, gff2gbsmalldna.pl, stringtie
Gin_x

Junior Member

Join Date: Sep 2015

Posts: 1
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#2

07-10-2021, 01:24 PM

Hi jinfang, I face the same issue you are missing max-size-of-gene-flanking-DNA, gff2gbSmall requires 3 parameters plus the output name <gff-file> <seq-file> and <max-size-of-gene-flanking-DNA> <output-name>

max-size-of-gene-flanking-DNA: specifies how much DNA is included around genes. The value 0 is fine if you want the output to contain only sequences of coding genes.
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