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  • 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
    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.

  • #2
    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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