├── LICENSE ├── README.md ├── img ├── QC.png ├── barcodes_format-01.png └── reads_plot.png ├── perlscripts ├── filt_mtx.pl ├── mergeBam.pl ├── merge_mtx.pl ├── sam2covFastq.pl └── split_bam.pl ├── pipeline ├── readme.md ├── run.sh └── scripts │ ├── bz2.sh │ └── gz.sh ├── protocol ├── Protocol_Github.pdf └── readme.md ├── reachtools ├── CMakeLists.txt ├── cxstring.cpp ├── cxstring.h ├── main.cpp ├── make.sh ├── reachtools.cpp ├── reachtools.h ├── readgenome.cpp ├── readgenome.h └── readme.txt ├── refereces ├── README.txt ├── cell_id_full.fa ├── cell_id_full_407.fa ├── hg38.RNA.txt ├── hg38.bin5k.txt ├── mm10.RNA.txt └── mm10.bin5k.txt.zip ├── remove_pileup ├── count_pileups.py ├── remove_pileups.py └── run.sh ├── rscripts ├── 2020_04_01_RNA_summary.xls ├── 2020_10_06_Paired-Tag_MetaData.xls ├── DNA_H3K4me1.R ├── H3K4me1.xls ├── Integration_H3K4me1.R ├── Paired-map.R ├── RNA_seurat.R ├── cxzhu.R └── plot_reads_numbers.R └── shellscrips ├── 01.pre_process_paired_tag_fastq.sh ├── 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