Difference between revisions of "Explaining My Project"
From GcatWiki
| Line 4: | Line 4: | ||
=Counting Kmers to Tell you about Genome= | =Counting Kmers to Tell you about Genome= | ||
(taken from https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish) | (taken from https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish) | ||
| + | [[File:Kmer.png]] | ||
| + | Bad kmer rate = bad multiplicity kmers/total number of all kmers | ||
| + | Seq Error Rate = bad kmer Rate/kmer size | ||
| + | Genome Coverage = use gamma fit on the good multiplicity values of the best kmer (usually largest). The peak of this line gives genome coverage (see red line) (here about 47.11x) | ||
| + | Genome size = number of unique good multiplicity kmers/coverage | ||
Revision as of 19:12, 3 June 2011
Shotgun Sequencing
Counting Kmers to Tell you about Genome
(taken from https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish)
Bad kmer rate = bad multiplicity kmers/total number of all kmers
Seq Error Rate = bad kmer Rate/kmer size
Genome Coverage = use gamma fit on the good multiplicity values of the best kmer (usually largest). The peak of this line gives genome coverage (see red line) (here about 47.11x)
Genome size = number of unique good multiplicity kmers/coverage
