getBestAlnInfo: Parse pairwise alignment

In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

Parse pairwise alignment

Description

Parse pairwise alignment

Usage

getBestAlnInfo(
  offtargetSeq,
  pa.f,
  pa.r,
  gRNA.size = 20,
  PAM = "NGG",
  PAM.size = 3,
  insertion.symbol = "^"
)

Arguments

offtargetSeq	DNAStringSet object of length 1
pa.f	Global-Local PairwiseAlignmentsSingleSubject, results of pairwiseAlignment, alignment of pattern to subject
pa.r	Global-Local PairwiseAlignmentsSingleSubject, results of pairwiseAlignment, alignment of pattern to reverse subject
gRNA.size	size of gRNA, default to 20
PAM	PAM sequence, default to NGG
PAM.size	PAM size, default to 3
insertion.symbol	symbol for representing bulge in offtarget, default to ^. It can also be set to lowerCase to use lower case letter to represent insertion

Value

a dataframe with the following columns. offTarget: name of the offtarget peak_score: place holder for storing peak score gRNA.name: place holder for storing gRNA name gRNAPlusPAM: place holder for storing gRNAPlusPAM sequence offTarget_sequence: offTarget sequence with PAM in the right orientation. For PAM in the 3' prime location, offTarget is the sequence on the plus strand otherwise, is the sequence on the reverse strand seq.aligned: the aligned sequence without PAM guideAlignment2OffTarget: string representation of the alignment offTargetStrand: the strand of the offtarget mismatch.distance2PAM: mismatch distance to PAM start n.PAM.mismatch: number of mismatches in PAM n.guide.mismatch: number of mismatches in the gRNA not including PAM PAM.sequence: PAM in the offtarget offTarget_Start: offtarget start offTarget_End: offTarget end chromosome: place holder for storing offtarget chromosome pos.mismatch: mismatch positions with the correct PAM orientation, i.e., indexed form distal to proximal of PAM pos.indel: indel positions starting with deletions in the gRNA followed by those in the offtarget pos.insertion: Insertion positions in the gRNA Insertion positions are counted from distal to proximal of PAM For example, 5 means the 5th position is an insertion in gRNA pos.deletion: Deletion in the gRNA Deletion positions are counted from distal to proximal of PAM For example, 5 means the 5th position is a deletion in gRNA n.insertion: Number of insertions in the RNA. Insertions in gRNA creates bulged DNA base n.deletion: Number of deletions in the RNA. Deletions in gRNA creates bulged DNA base

Author(s)

Lihua Julie Zhu

LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.