I have a couple of questions about the behaviour of mccortex31 subgraph.
Firstly, does --dist d specify the radius or diameter? i.e will subgraph extend from the input sequence a distance of d to the left and right (--dist specifies radius) or a distance of d/2 to the left and right (--dist specifies diameter)?
Secondly, if the sequence passed to --seq is a single kmer (of len 31 in this case), and
distance passed to --dist is d, if --dist specifies radius, is it the case that the maximum number of possible kmers that could be pulled from the original graph is4^d + 4^d + 1 (one 4^d term each for left and right extension, 1 for the original seed kmer) assuming each node in the de brujin graph has four edges?
Finally, if the sequence passed to --seq contains multiple uncontiguous kmers, will each of the kmers be extended a distance of d?
Kind regards, and thanks for any insight given!
Izaak Coleman
I have a couple of questions about the behaviour of
mccortex31 subgraph.Firstly, does
--dist dspecify the radius or diameter? i.e willsubgraphextend from the input sequence a distance ofdto the left and right (--distspecifies radius) or a distance ofd/2to the left and right (--distspecifies diameter)?Secondly, if the sequence passed to
--seqis a single kmer (of len 31 in this case), and distance passed to--distisd, if--distspecifies radius, is it the case that the maximum number of possible kmers that could be pulled from the original graph is4^d + 4^d + 1(one4^dterm each for left and right extension,1for the original seed kmer) assuming each node in the de brujin graph has four edges?Finally, if the sequence passed to
--seqcontains multiple uncontiguous kmers, will each of the kmers be extended a distance ofd?Kind regards, and thanks for any insight given! Izaak Coleman