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mccortex subgraph behaviour #87
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izaak-coleman
changed the title
mccortex subgraph behaviour
mccortex subgraph behaviour label:question
Aug 15, 2019
izaak-coleman
changed the title
mccortex subgraph behaviour label:question
mccortex subgraph behaviour
Aug 15, 2019
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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), anddistance 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
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