scripts for processing sci-CAR RNA-seq and ATAC-seq reads and downstream analysis
scATAC_seq folder includes scripts for processing sci-ATAC-seq part of sci-CAR (from fastq files to single cell ATAC-seq bam file after duplicated reads removal).
peak_count_sciATACseq folder includes scripts for gernerating single cell ATAC-seq peak count matrix for downstream analysis.
scRNA_seq_pipe includes scripts for processing sci-RNA-seq part of sci-CAR (from fastq files to single cell gene count matrix).
primer_sciRNA_ATAC_seq.xlsx include RT and PCR primers for sci-RNA-seq and sci-ATAC-seq (sci-CAR).