# Genome arithmetics

Aditya M Bhagwat

#### 2024-11-28

# Contents

# Introduction

This vignette discusses multicrispr’s genome arithmetics functionality, often required in the first step of Crispr/Cas9 design. Multicrispr’s genome arithmetics functions allow two-way transformations around a genomic range’s start/end. The GenomicRanges and plyranges packages also offer an extensive genome arithmetics functionality, though with functions designed as one-way transformations.

We illustrate the different operations on a small GRanges with four prime editing targets in Anazlone et al. (2019)

    require(multicrispr)
    bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
    gr <- char_to_granges(c(PRNP  = 'chr20:4699600:+',         # snp
                            HBB  = 'chr11:5227002:-',            # snp
                            HEXA = 'chr15:72346580-72346583:-',  # del
                            CFTR = 'chr7:117559593-117559595:+'),# ins
                         bsgenome = bsgenome)
    plot_intervals(gr, facet_var = c('targetname','seqnames'))

# Genome arithmetics

## Extend

    ext <- extend(gr, start = -10, end = +10, plot = TRUE)

## Up flank

    up <- up_flank(gr,  -22,  -1, plot=TRUE, facet_var=c('targetname', 'seqnames'))

## Down flank

    dn <- down_flank(gr, +1, +22, plot=TRUE)

## Double flank

    dbl <- double_flank(gr, -10,  -1, +1, +20, plot = TRUE)

    ##      8 flank ranges: 4 up + 4 down

# References

# Appendix

Anzalone, A.V., Randolph, P.B., Davis, J.R. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019). https://doi.org/10.1038/s41586-019-1711-4