MUSIC-tools (data analysis for MUSIC data)

1.Introduction

This repository includes major code we used to analyze MUSIC data associated with the manuscript: "Single-cell multiplex chromatin and RNA interactions in aging human brain" (Wen et al,. 2024)[].

2.MUSIC data library configuration

http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/intro.html#library-configuration.

3.Raw data processing

MUSIC derives a paired-end sequencing library which includes cell barcodes, complexes barcodes and DNA/RNA insert sequences. The first step to analyze MUSIC data requires extract all essential information from the paired-end fastq files. Step by step data processing documentation is here: http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/step.html.

3.1 MUSIC-docker

We developed a docker container called MUSIC-docker which is a wrapper of a Snakemake pipeline that enables raw data processing. A full documentation of MUSIC-docker can be found here: http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/index.html. You can also make your own updates and re-compile to build your own version of MUSIC-docker using source code here: https://github.com/Irenexzwen/MUSIC-docker

3.2 MUSIC Snakemake pipeline

If you are familiar with Snakemake pipeline, we also provided a Snakemake pipeline where you can update the config files according to your local working enviroment: https://github.com/Irenexzwen/MUSIC-Snakemake