Tissue-specific ATAC-seq peaks

In this repo, we provide Ery-specific and universal open chroamtin regions from an analysis 13 blood cell types, including 77 ATAC-seq data from PRJNA301969. Analysis method is adopted from: https://www.nature.com/articles/s41597-019-0071-0.pdf. Our code is provided in get_tissue_specific_peaks.ipynb. Briefly, ATAC-seq raw fastq files were downloaded from NCBI SRA using sra_download.py, ATAC-seq data was processed using HemTools atac_seq, and read count table was generated using diffPeaks.py. The output table is DiffPeak_yli11_2020-01-28.count_table.zip.

Results

Distribution of tissue specificity index

Tissue-specificity definition

H <= 3: Tissue-specific ATAC-seq peaks

H >= 3.5: Universal open chromatin

Ery-specific open chromatin: H<=3 & max read count tissue is Ery, containing 4518 peaks.

Correlation of the 77 ATAC-seq data using tissue-specific peaks

PCA plot of the 77 ATAC-seq data using tissue-specific peaks