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 d
specify the radius or diameter? i.e willsubgraph
extend from the input sequence a distance ofd
to the left and right (--dist
specifies radius) or a distance ofd/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
isd
, 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
(one4^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 ofd
?Kind regards, and thanks for any insight given! Izaak Coleman