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

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chip seq data analysis

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

Mar 07, 2023 470 likes •689 views

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

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ChIP-seq data analysis

Introduction to practicals I: data processing

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ENCODE Dataset

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

undifferentiated neuronal progenitor cells, and REST may act as a master negative regulator

f neurogenesis

+ corresponding inputs chr 1 & chr 2

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ChIP-seq data processing

Practicals

Downstream analysis

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ChIP-seq data processing

Practicals

Downstream analysis

ChIPQC deepTools vis ChIPseeker csaw Motifs Public resources Broad peaks Exo-spike

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ChIP-seq data processing

Practicals

Downstream analysis

ChIPQC deepTools vis ChIPseeker csaw Motifs Public resources Broad peaks Exo-spike

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Aligned reads .BAM merged peaks .BED

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

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

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

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

Strand cross-correlation

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

Strand cross-correlation Cumulative enrichment

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM Sample clustering .BED

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM Sample clustering .BED Integrative Genomic Viewer

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM Sample clustering .BED Integrative Genomic Viewer

duplicated reads black listed regions 1 x read coverage

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM Sample clustering .BED Integrative Genomic Viewer

duplicated reads black listed regions 1 x read coverage peaks calling

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM Sample clustering .BED Integrative Genomic Viewer

duplicated reads black listed regions 1 x read coverage peaks calling peaks intersecting

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM Sample clustering .BED Integrative Genomic Viewer

duplicated reads black listed regions 1 x read coverage peaks calling peaks intersecting peaks merging

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

Strand cross-correlation Cumulative enrichment Sample clustering .BAM Sample clustering .BED Integrative Genomic Viewer

duplicated reads black listed regions 1 x read coverage peaks calling peaks intersecting peaks merging

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