This repository contains the data-processing and bioinformatics analysis code used for the ESCC super-enhancer study. Raw and processed sequencing data are not included in the repository.
data_processing/: ChIP-seq, RNA-seq, ATAC-seq, and CUT&Tag processing code.figures/: analysis and plotting code grouped by main or supplementary figure number.
| Assay | Code |
|---|---|
| FASTQ trimming | data_processing/01_trim_fastq.sh |
| Single-end ChIP-seq | data_processing/chip_seq/01_align_filter_single_end.sh |
| Paired-end ChIP-seq candidate workflow | data_processing/chip_seq/02_align_filter_paired_end_candidate.sh |
| Enhancer/SE processing | data_processing/chip_seq/03_stitch_or_merge_regions.sh, data_processing/chip_seq/04_quantify_regions.sh, and data_processing/chip_seq/05_identify_super_enhancers.Rmd |
| RNA-seq | data_processing/rna_seq/01_star_rsem.sh |
| ATAC-seq | data_processing/atac_seq/01_bam_to_bigwig.sh and supporting R scripts in the same directory |
| CUT&Tag | data_processing/cut_tag/01_align_spikein.sh through data_processing/cut_tag/03_align_hg19_and_scale.sh |
Code is grouped in figures/Figure_1 through figures/Figure_6 and
figures/Supplementary_Figure_S1.