alignShortReads {R453Plus1Toolbox} | R Documentation |
This method aligns given sequences against a given reference
genome using the matchPDict
method. Only exact (no errors) and unique
matches are returned.
alignShortReads(object, bsGenome, seqNames, ensemblNotation)
object |
The reads that should be aligned agiven either as a
|
bsGenome |
A |
seqNames |
The names of the sequences in |
ensemblNotation |
If set to TRUE, “chr” is removed from the reference sequences' names in the returned alignment. Default value is FALSE. |
All reads are aligned against the reference and its reverse
complement. If the reads are not in 5' to 3' orientation, they should
be reversed before. Note that only exact and unique alignments are
reported. Use matchPDict
directly for more flexibility.
An object of class AlignedRead
or a AVASet
instance.
Hans-Ulrich Klein
matchPDict
, DNAStringSet
,
AlignedRead
, AVASet
library("BSgenome.Scerevisiae.UCSC.sacCer2") reads = DNAStringSet(c( "CCGTTCAAAGAGCCCTTGGCCCATAATCCACCGGTT", "ATCCTGCCACAGGAGTCCATGGAGGTTTCGCCA")) alignShortReads(reads, Scerevisiae, seqNames="chrIII")