Refactor code that find kmers in genome/BGCs

sdrogers / amr

AMR

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Refactor code that find kmers in genome/BGCs #7

Open 2064240P opened 4 years ago

sdrogers commented 4 years ago

Maybe also worth searching for known resistance genes (they have them in Patric) in the vicinity of Kmers

sdrogers commented 4 years ago

think that it's best to map them both to the genome (by both I mean the Kmers and the BGCs) and then look for proximity

2064240P commented 4 years ago

BGCs do have coordinates in the genome, so I guess it's more once we have the coordinates of the kmers check for overlap

youngfran commented 4 years ago

The finding kmers notebook finda a list of kmers in a list of genomes. I will check what I did , I can't remember what I dd about kmers in the the reverse strand and that dsk only stores one half of the compliments.

youngfran commented 4 years ago

I will also have a look at getting a list of resitance gene positions for each genome.