These are collected scripts that constitute a pipeline to analyse Cut and Run / Cut and Tag datasets. The scripts have been taken from the tutorial put together by Ye Zheng, Kami Ahmad and Steven Henikoff. The scripts have been modified to facilitate processing - see below for further details.

Use FASTQC and FastQ Screen.

Use trim galore if reads >25bp

Pipeline details: https://yezhengstat.github.io/CUTTag_tutorial/

Input fastq files need to be of the format when passing to the pipeline

[sample_name]_rep[1,2,3,...n].fastq.gz

No underscores are allowed in the sample_name.

wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faSize

./faSize -detailed -tab file.fasta

Place FASTQ files in a folder named 'fastq'

nohup bash ./mapping.sh > log.mapping.sh.log &

nohup bash ./spike_in.sh > log.spike_in.sh.log &

Rscript alignment_summary.R

nohup bash analyse_duplicates.sh > log.analyse_duplicates.sh.log &

Rscript summarise_duplicates.R

nohup bash analyse_frag_size.sh > log.analyse_frag_size.out &

Rscript summarise_frag_length.R

nohup bash filter_quality.sh > log_filter_quality.sh.log &

nohup bash file_format_conversion.sh > log.file_format_conversion.sh.out &

nohup bash correlation_matrix.sh > log.correlation_matrix.sh.out &

Rscript correlation_matrix.R

nohup bash spike_in_calibration.sh > log.spike_in_calibration.sh.out &

Rscript spike_in_calibration.R

nohup bash peak_calling.sh > log.peak_calling.sh.out &

Rscript summarise_peaks.R

nohup bash visualisation.sh > log.visualisation.sh.out &