no control_kmers.fasta file

atifrahman / HAWK

Hitting associations with k-mers

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no control_kmers.fasta file #14

Open dstern opened 5 years ago

dstern commented 5 years ago

HAWK has apparently run successfully on my data and I have an interesting case_kmers.fasta file that I could assemble with ABYSS. However, no control_kmers.fasta file was produced. Any thoughts on why and how to recover it?

atifrahman commented 5 years ago

Cool!

It can be due to two reasons:

If the phenotype of the cases is due to presence of some sequence, then there is sequence associated with cases but not with controls. This was the case with the E. coli ampicillin resistance dataset we tested on.
If the number of controls is small then the k-mers associated with controls may not have low enough p-values to show up in the output.