when using deeptools computeMatrix, you wont be able to get the central point "central", you need to shift the point half the binsize, and add a new bin

shiftandmove_reference_for_computeMatrix.r

#!/usr/bin/env Rscript
suppressPackageStartupMessages({
    library(tidyverse)
})
args <- commandArgs(trailingOnly = TRUE)
bed <- args[1]
distshift <- args[2] %>% as.numeric()
chromsize <- args[3]

# debug only
# bed <- "ERV1.bed"
# distshift <- 2500
# chromsize <- "../GRCm38_2019/GRCm38_2019_tdt/chrNameLength.txt"

chromsize <- read_table(chromsize,
    col_names = c("seqnames", "length"),
    col_types = cols()
)
chromsize_ <- chromsize$length
names(chromsize_) <- chromsize$seqnames
chromsize <- chromsize_
rm(chromsize_)

splitandshiftplusminus <- function(bed) {
    bedname <- bed %>% str_remove(".bed")
    df <- read_table(bed, col_names = c(
        "seqnames",
        "start",
        "end",
        "name",
        "score",
        "strand"
    ), col_types = cols()) %>%
        rowwise() %>%
        mutate(
            shift_dist = case_when(
                strand == "+" ~ distshift,
                strand == "-" ~ -distshift,
                TRUE ~ distshift
            ),
            new_start = start + shift_dist,
            new_start = case_when(
                new_start < 0 ~ 0,
                new_start > (chromsize[seqnames] - 1) ~
                (chromsize[seqnames] - 1),
                TRUE ~ new_start
            ),
            new_end = new_start + 1,
            strand = factor(
                strand,
                levels = c("+", "-"),
                ordered = TRUE
            )
        ) %>%
        select(c(
            seqnames,
            new_start,
            new_end,
            name,
            score,
            strand
        )) %>%
        rename(start = new_start, end = new_end) %>%
        ungroup()
    df %>%
        group_split(strand) %>%
        imap(function(df, name) {
            if (name == 1) {
                filename <- paste0(bedname, "_plus.bed")
            } else if (name == 2) {
                filename <- paste0(bedname, "_minus.bed")
            } else {
                stop("strand not found")
            }
            df %>% write_tsv(file = filename, col_names = FALSE)
        })
    return(NULL)
}
splitandshiftplusminus(bed)