gene_presence_absence table

[meiym-012]

Hi,

I've used scoary to find gene present/absent in bacteria genomes. I found many genes recorded as "absent" in the gene_presence_absence.csv were actually present when I blastn the gene sequence with the assembled fasta file, or grep the gene name in the prokka annotated gff format file. Could you help me understand what happens?

This is my command line:

prokka --outdir ~/output/prokka/002 --locustag 002 --proteins ~/refseq/NC_000962.3/NC_000962.3.gb --kingdom Bacteria --gcode 11 --cpus 64 ~/input/assembly/002.contig.fasta ...... cp ~/output/prokka/002/002.gff ~/output/prokka/gff_100 roary -p 64 -e -n -r -v -f ~/output/roary/cohort_100/ ~/output/prokka/gff_100/*.gff python ~/soft/Roary-master/contrib/roary_plots/roary_plots.py accessory_binary_genes.fa.newick gene_presence_absence.csv

Many thanks

Mei