Data Wrangling - Convert S.namaycush NCBI GFF to genes-only BED file for Use in Ballgown Analysis

In preparation for isoform identificaiton/quantification in S.namaycush RNAseq data, Ballgown will need a genes-only BED file. To generate, I used GFFutils to extract only genes from the NCBI GFF: GCF_016432855.1_SaNama_1.0_genomic.gff. All code was documented in the following Jupyter Notebook.

Jupyter Notebook

• GitHub

• NBViewer

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RESULTS

Output folder:

• 20220818-snam-gff_to_bed-genes/

  • BED file (2.2MB)

    • 20211209_cvir_gff-to-bed/20220818-snam-GCF_016432855.1_SaNama_1.0_genes.bed

      • MD5 checksum:

        • 440d09ac4bd225a6585d69ef623fd812

The resulting BED file was added to the Roberts Lab Handbook - Genomic Resources page.