ChIP-seq data analysis Introduction to practicals I: data processing - PowerPoint PPT Presentation

ChIP-seq data analysis Introduction to practicals I: data processing

ENCODE Dataset chr 1 & chr 2 • REST is transcriptional repressor that represses neuronal genes in non-neuronal cells • It represses transcription by binding a DNA sequence element called neuron-restrictive silencer element (NRSE) • The protein is also found in undi ff erentiated neuronal progenitor cells, and REST may act as a master negative regulator of neurogenesis + corresponding inputs

Practicals ChIP-seq data processing Downstream analysis

Practicals ChIPQC Broad peaks deepTools vis ChIP-seq data processing Downstream analysis Motifs csaw Public ChIPseeker resources Exo-spike

Practicals ChIPQC Broad peaks deepTools vis ChIP-seq data processing Downstream analysis Motifs csaw Public ChIPseeker resources Exo-spike

Aligned reads .BAM merged peaks .BED

Aligned reads .BAM Processed alignment .BAM merged peaks .BED

Aligned reads .BAM Processed alignment .BAM Peaks .BED merged peaks .BED

Aligned reads .BAM Processed alignment .BAM Peaks .BED reproducible peaks .BED merged peaks .BED

Aligned reads .BAM Strand cross-correlation Processed alignment .BAM Peaks .BED reproducible peaks .BED merged peaks .BED

Aligned reads .BAM Strand cross-correlation Processed alignment .BAM Cumulative enrichment Peaks .BED reproducible peaks .BED merged peaks .BED

Aligned reads .BAM Strand cross-correlation Processed alignment .BAM Cumulative enrichment Peaks .BED reproducible peaks .BED Sample clustering .BAM merged peaks .BED

Aligned reads .BAM Strand cross-correlation Processed alignment .BAM Cumulative enrichment Peaks .BED reproducible peaks .BED Sample clustering .BAM merged peaks .BED Sample clustering .BED

Aligned reads .BAM Strand cross-correlation Processed alignment .BAM Cumulative enrichment Peaks .BED reproducible peaks .BED Sample clustering .BAM Integrative Genomic Viewer merged peaks .BED Sample clustering .BED

duplicated reads black listed regions Aligned reads .BAM 1 x read coverage Strand cross-correlation Processed alignment .BAM Cumulative enrichment Peaks .BED reproducible peaks .BED Sample clustering .BAM Integrative Genomic Viewer merged peaks .BED Sample clustering .BED

duplicated reads black listed regions Aligned reads .BAM 1 x read coverage Strand cross-correlation Processed alignment .BAM peaks calling Cumulative enrichment Peaks .BED reproducible peaks .BED Sample clustering .BAM Integrative Genomic Viewer merged peaks .BED Sample clustering .BED

duplicated reads black listed regions Aligned reads .BAM 1 x read coverage Strand cross-correlation Processed alignment .BAM peaks calling Cumulative enrichment Peaks .BED peaks intersecting reproducible peaks .BED Sample clustering .BAM Integrative Genomic Viewer merged peaks .BED Sample clustering .BED

duplicated reads black listed regions Aligned reads .BAM 1 x read coverage Strand cross-correlation Processed alignment .BAM peaks calling Cumulative enrichment Peaks .BED peaks intersecting reproducible peaks .BED peaks merging Sample clustering .BAM Integrative Genomic Viewer merged peaks .BED Sample clustering .BED

duplicated reads black listed regions Aligned reads .BAM 1 x read coverage Strand cross-correlation Processed alignment .BAM peaks calling Cumulative enrichment Peaks .BED peaks intersecting reproducible peaks .BED peaks merging Sample clustering .BAM Integrative Genomic Viewer merged peaks .BED Sample clustering .BED