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)
The reads that should be aligned agiven either as a
The names of the sequences in
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
matchPDict directly for more flexibility.
An object of class
AlignedRead or a
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