Included in this GitHub are example scripts for analyzing CUT&RUN datasets and peak files from previously published ChIP-seq datasets (peaks were called using HOMER)
Here is the general pipeline for analysis:
1) trim reads to 25 bases (while keeping paired)
2) split reads using novocraft (also trims off barcode with -l option)
3) Align reads using Bowtie2 (align to yeast or to mouse)
4) Remove duplicate reads (created through PCR) using Picard
5) Remove low quality reads (MAPQ <10)
6) Make Size Distribution file for mm10
6B) Make size distribution for sacCer3, spike in
7) Make size classes (1-120 for TF, 150-500 for histones)
8) Homer analysis
makeTagDirectory
makeUCSCfile
make aggregation plots or heatmaps over specific anchor location
call peaks
find motifs