A nucleosomal reads counting tool
Nucount is an R tool for estimating ChIP-seq reads from positioned nucleosomes. Adjacent reads will be assigned by Expectation Maximization approach.
R 4.1.2: optparse, dplyr, S4Vectors, Rsamtools, rtracklayer, GenomeInfoDb, BiocGenerics, IRanges, foreach, doParallel, ggplot2.
See the help messages:
Rscript Nucount_script.R -h
You can test Nucount with the example.
#!/bin/bash -l
Rscript Nucount_script.R \
-b 'example/bam/H3K4me3_GSM2417080_Chronis_example.bam' \
-p FALSE \
-n 'example/nuc_fltd_gr_mm9_20.RData' \
-t 'example/tss_mm9_gr.RData' \
--is_EM TRUE --iter_num 2 \
-o 'H3K4me3_test' --type 'bw' \
--quietly FALSE