Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) for simultanouse chromatin, RNA-chromatin and transcriptome mapping at single cell resolution

MUSIC manuscript: Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain. MUSIC-docker is the customized pipeline to process the raw fastq files to bam files: http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/intro.html. Each bam file records the final output of our single cell mixed species analysis. Read name recods the cell barcode, complex barcode and I7 index. For each DNA/RNA read, read header contains raw read name| BC3_BC2_BC1 - 10x barcode # UMI. Details of the read name can be found here: http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/step.html#demultiplexing. merge_DNA [RNA]_human [mouse].sort.bam: bam file of DNA [RNA] reads from the mix species library (H1+E14) that can uniquely mapped to the human [mouse] genome. PCR duplicates have been removed.