Partitioning the yeast genome
Genomes are often big, but interest usually lies in specific regions of them. Therefore, we need to subset a genome by extracting parts of it. To pick a sequence interval, use getSeq() and specify the name of the chromosome and the start and end of the sequence interval.
The following example will select the bases of "chrI" from 100 to 150.
getSeq(yeastGenome, names = "chrI", start = 100, end = 150)
Note: names is optional; if not specified, it will return all chromosomes. The parameters start and end are also optional and, if not specified, will take the default values 1 and the length of the sequence, respectively.
Cet exercice fait partie du cours
Introduction to Bioconductor in R
Instructions
- Use
getSeq()to get the first 30 bases of the M chromosome ("chrM") in theyeastGenomeobject.
Exercice interactif pratique
Essayez cet exercice en complétant cet exemple de code.
# Load the yeast genome
library(BSgenome.Scerevisiae.UCSC.sacCer3)
# Assign data to the yeastGenome object
yeastGenome <- BSgenome.Scerevisiae.UCSC.sacCer3
# Get the first 30 bases of chrM
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