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SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
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understanding pirate results #88

Closed happymanmohit closed 2 weeks ago

happymanmohit commented 4 months ago

Hii I ran a pangenome analysis for 7 genomes using bacteria, which used Pirate for the pangenome analysis and gave results as pirate unique alleles, gene presence_absence. Now, it is very hard for me to understand the output. Can you please suggest how to find which genes are absent or present in a particular genome?

SionBayliss commented 2 weeks ago

Hi Mohit,

The description of the output formats can be found in the README under the 'PIRATE.*.tsv file format' section. There is a series of columns at the end of each file which correspond to your input genomes. The gene_presence_absence file is the one you should be looking at.

S