Talk:Subset genes, pan- and core genomes/@comment-202.20.103.137-20150701065334

hi,

I have a dataset of 46 genomes and have used CMG-biotools to analyze their pan- and core-genomes. When calculating subset genes present in one particular genome, lets call it genome "X", using a similar code to the example above "specificGenes -i 1:3,5:7", the number of gene sequences results in "0". Also, when I tried to calculate the subset of genes for a group of 19 genomes that has this particular genome (with 0 unique genes), the result for the entire group is also "0" gene sequences. This is odd because the script works perfectly well for any combination of genomes that does not include genome "X".

I have investigated the file for genome X and there does not seem to be anything questionable about it. There should really be no reason why a single genome in a dataset of 46 genomes can produce 0 gene sequences when using this script. I should mention that all 46 genomes belong to bacteria of the same species.

Can you provide some guidance on this issue please?

Many thanks,

N