To walk through the pipeline quickly, we make an small example of GATA1 CUT&RUN dataset from our paper only containing data from chromosome 11 (can be found in the folder exampleData ) to illustrate the usage of our bulk data analysis pipeline. It will take roughly less than half an hour to run the entire pipeline from raw sequencing data using a laptop with 4 cores.
Download the example data with two fastq files suffix with R1_001.fastq.gz, and R2_001.fastq.gz in the exampleData folder.
To configure the exampleData_configure.sh file:
specify the workdir;
specify the fastqdir parameter as the folder of exampleData;
make sure you have successfully installed pre-requsite software, set the paths and validate the bulk-config.json file ;
Then you can simply run the following command to perform the entire pipeline.
# Usage:
# ./run_bulkModule.sh configure.json sample_name
chmod +x ./run_bulkModule.sh
./run_bulkModule.sh /path/to/bulk-config.json GATA1_D7_30min_chr11
What happens next is that CUT&RUNTools 2.0 will sequentially run the analysis pipeline, see the Usages and output Directory Structure for details.