ATAC-Seq Data Processing & Comparison with DNase-Seq
The content discusses the comparison and processing of ATAC-seq and DNase-seq data, including peak calling, summary, peak size, overlapping peaks, and examples from studies. It also mentions specific labs where the data were generated, the number of tissue samples analyzed, and the pipeline used for data processing.
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Presentation Transcript
ATAC ATAC- -seq comparison comparison with seq data data processing processing & & with DNase DNase- -seq seq Min Xu @Gerstein Lab, Yale University
ATAC ATAC- -seq seq & DNase & DNase- -seq seq data data summary summary ENC-001 ENC-002 ENC-003 ENC-004 Age 37 54 53 51 Sex Male Male Female Female Tissue samples for ATAC-seq 6 12 13 15 Tissue samples for DNase-seq 13 10 17 16 Matching tissues 6 10 9 12 The ATAC-seq data were generated by Michael Synder s lab; The DNase-seq data were generated by John Stamatoyannopoulos s lab; Some data here are missing because of being revoked or archived.
ATAC ATAC- -seq seq peak calling peak calling Current data Pipeline used (unreplicated data): developed by Anshul Kundaje s lab All the ATAC-seq data were processed locally for ENC-002 and ENC-003; other data will be processed soon.
ATAC ATAC- -seq seq data data & & peak summary peak summary 1e8
ATAC ATAC- -seq seq peak size peak size DNase-seq peak size DNase-seq peak size is always 150, which is the minimal size for the ATAC- seq peaks Tissue 150 Size
(>= 1 bp) Fraction
(>= 1 bp) Fraction
High High- -confident ATAC confident ATAC- -seq seq peaks overlapping with DNase peaks overlapping with DNase- -seq seq peaks peaks Overlapping Fraction 1.0 Fraction of top high-confident peaks
Examples: ENC Examples: ENC- -003 003 transverse transverse colon colon Good overlap No overlap ATAC-seq signal Dnase-seq signal *Zhiping Weng
Result from another study Result from another study Human K562 cell line JAMM was used to call the peaks Shows more overlap than our data Karabacak Calviello, A. et al, bioRxiv(2018). https://doi.org/10.1101/284364
Further validation Further validation ATAC overlapping with DNase DNase overlapping with ATAC Entex individuals (various tissues) DNase-seq samples (frontal cortex) ENC002: 6 samples ENC003: 8 samples Pairwise comparison ATAC-seq: 292 samples (BrainGVEX) DNase-seq: 4 samples (Encode) 292 to 1 comparison
Summary Summary All the ATAC-seq data were processed for ENC-002 and ENC-003 More ATAC-seq peaks can be overlapped with DNase-seq peaks than the other way around. Higher-confident peaks are more likely to be overlapped with DNase- seq peaks.
