Extract list of genes for annotated contig

1

Hi,

I processed E. coli genome using standard pipeline (Unicycler) and annotated it using Prokka. Pasted below are first few lines from GFF file:
##gff-version 3
##sequence-region 1 1 2860445
##sequence-region 2 1 1613318
##sequence-region 3 1 142357
##sequence-region 4 1 17570
##sequence-region 5 1 3029
##sequence-region 6 1 1797
##sequence-region 7 1 563
##sequence-region 8 1 331
##sequence-region 9 1 224

My colleague needs a list of genes on 3rd contig (i.e., sequence-region 3). How should I proceed? My idea is to select all rows that belong to 3rd contig from GFF file (using filter “Seqname == 3”), extract identifier (e.g., “FADBEKOL_00002”) from last, “Group”, field and join output with TSV file from Prokka.

Any other idea is greatly appreciated.

Best, Andrej

3

2026 Update! Any text data can be parsed! Search under Text Manipulation for GFF-data specific options or try one of these → :graduation_cap: Hands-on: Data Manipulation Olympics / Data Manipulation Olympics / Introduction to Galaxy Analyses