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Old 08-14-2019, 12:08 PM   #1
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Location: lincoln

Join Date: Jul 2019
Posts: 1
Angry gff2gbSmall

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 stringtie.gff gene.fasta

However, I got nothing in

Anyone guys who know why I got an empty file.

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Old 07-10-2021, 01:24 PM   #2
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Location: Canada

Join Date: Sep 2015
Posts: 1

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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augustus, genbank, gff,, stringtie

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