SCENIC+ Tutorial

Download 10X output

#!/bin/bash

samples=("s1" "s2")
# Base URL for download
base_url="https://XXX/counts"

# Directory paths

download_dir="/volume/data/XXX/raw"

for sample in "${samples[@]}"
do
    echo "Processing sample: $sample"

    # Create a directory for the sample
    mkdir -p "$download_dir/$sample"
    
    # Download the folder contents
"$download_dir" "$base_url/$sample/outs/"

    wget -r -nc -np -nH --cut-dirs=6 -P "$download_dir/$sample" "$base_url/$sample/outs/filtered_feature_bc_matrix.h5"
    wget -r -nc -np -nH --cut-dirs=6 -P "$download_dir/$sample" "$base_url/$sample/outs/atac_fragments.tsv.gz"
    wget -r -nc -np -nH --cut-dirs=6 -P "$download_dir/$sample" "$base_url/$sample/outs/atac_fragments.tsv.gz.tbi"
    
    echo "Finished downloading $sample"
done

Scanpy Preprocessing

Get pycisTopic Object

Set-up and Run SCENIC+