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

<p><a href="https://doi.org/10.1101/2023.06.28.546457">MUSIC manuscript:</a>&nbsp;Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain.</p> <p>MUSIC-docker is the customized pipeline to process the raw fastq files to bam files:&nbsp;http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/intro.html.</p> <p>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&nbsp;<code>raw&nbsp;read&nbsp;name</code>|&nbsp;<code>BC3</code>_<code>BC2</code>_<code>BC1</code>&nbsp;-&nbsp;<code>10x&nbsp;barcode</code>&nbsp;#&nbsp;<code>UMI</code>. Details of the read name can be found here:&nbsp;http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/step.html#demultiplexing.</p> <p>merge_DNA [RNA]_human [mouse].sort.bam: bam file of DNA [RNA] reads from the mix species library (H1+E14)&nbsp;that can uniquely mapped to the human [mouse] genome. PCR duplicates have been removed.&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p>