Explaining My Project - Revision history

Letaylor: /* Counting Kmers to Tell you about Genome */

2011-06-08T20:30:32Z

‎Counting Kmers to Tell you about Genome

2011-06-03T19:12:45Z

‎Counting Kmers to Tell you about Genome

2011-06-03T19:12:14Z

2011-06-03T19:02:27Z

2011-06-02T14:30:55Z

Created page with 'File:Shotgun.png'

New page

[[File:Shotgun.png]]

← Older revision		Revision as of 20:30, 8 June 2011
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	*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 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		*Genome size = number of unique good multiplicity kmers/coverage
		+	*1st peak (@ low multiplicity) = from seq errors
		+	*2nd peak = multiple copies of the same location in the genome
		+	**If a k-mer occurs n times in the genome, we would expect to see it n times as often in the sequencing, so there should be additional peaks for k-mers that occur in repeats.

@@ Line 5: / Line 5: @@
 (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
+*Bad kmer rate = bad multiplicity kmers/total number of all kmers
-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)
+*Seq Error Rate = bad kmer Rate/kmer size
-Genome size = number of unique good multiplicity kmers/coverage
+*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)

← Older revision		Revision as of 19:12, 3 June 2011
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	=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

← Older revision		Revision as of 19:02, 3 June 2011
Line 1:		Line 1:
		+	=Shotgun Sequencing=
	[[File:Shotgun.png]]		[[File:Shotgun.png]]
		+
		+	=Counting Kmers to Tell you about Genome=
		+	(taken from https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish)