This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to find singletons in get_homologues

Hi I'm new to bioinformatics (i'm undergrad). I have 2 genomes, same species, probably different strains. I've used get_homologues to define the core genome, but i'm having trouble to find the singletons. I have already read several times both the manual and tutorial available and i've tried to used parse_pangenome_matrix to find which genes are present in A and absent in B, and it seems that there isn't any! (file with genes present in set A and absent in B (0) ).

How can it be possible, if the core genome is smaller than both genomes?

sequence gene
• 1,404 views • link
updated by Tm Tm • written by deboraguerrapeixe • deboraguerrapeixe

If they are the same species this is not so surprising.

• 1 views • link
written by lieven.sterck lieven.sterck

1 answer

If you have a core gene set and complete gene set, then you can consider subtracting core genes from complete gene set using simple shell command.

For instance, 

grep -w -v -f core_gene_set.txt complete_gene_set_sampleA.txt >singleton_sampleA.txt
grep -w -v -f core_gene_set.txt complete_gene_set_sampleB.txt >singleton_sampleB.txt

Here,

  1. -w, means it will search for exact word provided in core gene set file from the complete_gene_set.txt file
  2. -v, means it will search for non-matching lines provided in core gene set file from the complete_gene_set.txt file
  3. -f, means it will grep PATTERN provided in core gene set file from complete_gene_set.txt file
• 1 views • link
written by Tm Tm

Log in to answer this question.

More posts like this