ilead-cong / sciDLO

sciDLO Hi-C

Single cell indexed DLO Hi-C analysis pipeline.

Install

1. Install DLO-HiC-Tools.
2. Install Nextflow(version >= 20.07.1.5412)
3. Clone this repo, and compile the extpet tool.

# Install Rust
$ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
$ export PATH=$PATH:~/.cargo/bin  # add cargo path to the PATH env variable
# Compile
$ cd scTools; cargo build --release

4. Add export PATH=<path_the_repo>/scripts:$PATH to the end of your .bashrc.

Run pipeline

1. Copy main.nf and nextflow.config to your working path.
2. Modify nextflow.config.
3. Run nextflow run main.nf.

Result

Result file of each steps will stored in the result folder in the working path.

sub folder	description
pairs_cell	pairs of each cell
pairs_lib	pairs of each library
pairs_all	merged pairs
dot_hic_cell	.hic file of each cell
dot_hic_lib	.hic file of each library
dot_hic_all	.hic file of all merged reads
tmp	intermediate files of each steps