Comments (2)
Hi,
Thanks for using KMC!
In most applications, k-mer and its reverse complement should not be distinguished.
Simply speaking for each k-mer its reverse complement is calculated.
Canonical k-mer is a lexicographically smaller of two (k-mer and its reverse complement). KMC in default mode counts only canonical k-mers.
If you need k-mers as they are, there is an -b option. Then for you sequence the output is:
Stage 1: 100%
1st stage: 0.0552348s
2nd stage: 0.0376972s
Total : 0.092932s
Tmp size : 0MB
Stats:
No. of k-mers below min. threshold : 0
No. of k-mers above max. threshold : 0
No. of unique k-mers : 34
No. of unique counted k-mers : 34
Total no. of k-mers : 51
Total no. of sequences : 1
Total no. of super-k-mers : 0
There are in fact 34 k-mers:
AAA 3
AAT 4
AGC 1
ATA 2
ATC 2
ATG 2
CAA 1
CCA 1
CCC 1
CCT 1
CGA 1
CGC 4
CTA 2
CTC 1
CTG 1
GAT 1
GCC 1
GCG 2
GCT 2
GGG 1
GGT 1
GTC 1
GTT 1
TAA 2
TAG 1
TAT 1
TCC 1
TCG 3
TCT 1
TGC 1
TGG 1
TGT 1
TTC 1
TTT 1
If you agree and have no questions please close this issue, in the opposite case let me know what is not clear.
from kmc.
Yes, that clears things up. Thanks!
from kmc.
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