sc-QUICK.md

Example for single-cell data analysis

Easy 1-step execution

We used a published single-cell CUT&Tag dataset which detected the H3K27me3 signal of individual H1 and K562 cells (Kaya-Okur, et al. Nat Commun 10, 1930 (2019)), as an example to illustrate the utility and functionality of our tool. To walk through the pipeline quickly, we make an small example dataset only containing data from chr11 of 200 cells (can be found in the folder exampleData), by randomly selecting 100 cells for the two cell types, respectively. It will take roughly half an hour to run the entire pipeline from raw sequencing data using a laptop with 8 cores.

Download and uncompress the exampleData.tar.gz

tar -zxvf exampleData-sc.tar.gz

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 (make sure to set both of percentage_rip and num_reads_threshold as 0, and set matrix_type as bin_by_cell when you use the example data)

Then you can simply run the following command to perform the entire pipeline.

chmod +x ./run_scModule.sh   
./run_scModule.sh /path/to/sc-config.json

What happens next is that CUT&RUNTools will sequentially run the analysis pipeline, see the Usages and output Directory Structure for details.