Understanding the -k parameter

[antunderwood]

Understanding the -k parameter

[tobiasrausch]

-k sets the initial k-mer length. With default options, dicey enumerates the neighborhood of this k-mer at edit distance 1 and then searches these k-mers in the genome for all exact matches. For non-unique 15-mers that occur abundantly in the genome this search may return >>10,000 matches that dicey then evaluates as possible binding sites. To speed up this search, the online version only evaluates at most 10,000 matches. On the command-line, you can force dicey to evaluate all matches using -m 10000000 but this may cause a long runtime of the program. A 20-mer is more unique in the genome and thus, less candidate hits need to be evaluated.

[tobiasrausch]

Closing this issue here because of gear-genomics/dicey#11.