uniqueCleavageEvents: example unique cleavage sites

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

example unique cleavage sites

Description

An example data set containing cleavage sites with unique UMI, generated from getUniqueCleavageEvents

Value

cleavage.gr

Cleavage sites with one site per UMI as GRanges with metadata column total set to 1 for each range

unique.umi.plus.R2

a data frame containing unique cleavage site from R2 reads mapped to plus strand with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) start.y (start of readSide.y/R2 read) end.x (start of readSide.x/R1 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

unique.umi.minus.R2

a data frame containing unique cleavage site from R2 reads mapped to minus strand with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) end.y (end of readSide.y/R2 read) start.x (start of readSide.x/R1 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

unique.umi.plus.R1

a data frame containing unique cleavage site from R1 reads mapped to minus strand without corresponding R2 reads mapped to the plus strand, with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) start.x (start of readSide.x/R1 read) start.y (start of readSide.y/R2 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

unique.umi.minus.R1

a data frame containing unique cleavage site from R1 reads mapped to plus strand without corresponding R2 reads mapped to the minus strand, with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) end.x (end of readSide.x/R1 read) end.y (end of readSide.y/R2 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

all.umi

a data frame containing all the mapped reads with the following columns. readName (read ID), chr.x (chromosome of readSide.x/R1 read), start.x (start of eadSide.x/R1 read), end.x (end of eadSide.x/R1 read), mapping.qual.x (mapping quality of readSide.x/R1 read), strand.x (strand of readSide.x/R1 read), cigar.x (CIGAR of readSide.x/R1 read) , readSide.x (1/R1), chr.y (chromosome of readSide.y/R2 read) start.y (start of readSide.y/R2 read), end.y (end of readSide.y/R2 read), mapping.qual.y (mapping quality of readSide.y/R2 read), strand.y (strand of readSide.y/R2 read), cigar.y (CIGAR of readSide.y/R2 read), readSide.y (2/R2) R1.base.kept (retained R1 length), R2.base.kept (retained R2 length), distance (distance between mapped R1 and R2), UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

Source

http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1695644

Examples

    data(uniqueCleavageEvents)
    names(uniqueCleavageEvents)
    sapply(uniqueCleavageEvents, class)
    uniqueCleavageEvents[[1]]  # GRanges object
    lapply(uniqueCleavageEvents, dim)

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