--- tags: GeneLab title: Converting GenBank format to gtf --- # Converting GenBank format to gtf **Creating conda environment** ```bash conda create -y -n conv-gb-to-gtf -c conda-forge -c bioconda -c defaults perl-bioperl=1.6.924 perl-lwp-protocol-https=6.10 perl-yaml=1.30 gffread=0.12.7 conda activate conv-gb-to-gtf ``` **Getting and gunzipping example gbff file** ```bash curl -LO https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/008/865/GCA_000008865.2_ASM886v2/GCA_000008865.2_ASM886v2_genomic.gbff.gz gunzip GCA_000008865.2_ASM886v2_genomic.gbff.gz ``` **Converting from GenBank to GFF3 then GFF3 to GTF** ```bash bp_genbank2gff3 GCA_000008865.2_ASM886v2_genomic.gbff gffread GCA_000008865.2_ASM886v2_genomic.gbff.gff -T -o GCA_000008865.2_ASM886v2_genomic.gtf ```
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Mike Lee
microbialomics.org/research github.com/AstrobioMike
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