R and bash scripts to analyse CUT&Tag data using Signac, Deeptools, MACS2, SEACR and more.
Link to Google docs of bulleted pipeline steps
This folder contains the "mother" scripts, which have then been copied to the analysis folders such as /H3K27ac_VMH_ExptD and amended as appropriate to filter and set ie clustering resolution.
Note that in current state it's necessary to set the path to ie. fastq and hashtag fastq in both 00_parameters and in each bash script.
cutntag.yml contains conda environment with all the necessary packages.
I found it useful to invoke the scripts in this manner:
R -e "rmarkdown::render('03_demultiplex.Rmd',output_file='03_demultiplex.html')"
bash -x 04_filteredCells_makeBAMmakeBWfindPeaks.sh &> logfile_04.log
Link to write-up about cutNtag in general and some thoughts on it.