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Book Cover
E-book
Author Mifsud, Borbala

Title Practical Guide to ChIP-Seq Data Analysis
Published Milton : Chapman and Hall/CRC, 2018

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Description 1 online resource (112 pages)
Series Focus Computational Biology Ser
Focus Computational Biology Ser
Contents Cover; Half Title; Title Page; Copyright Page; Preface; Authors; Table of Contents; CHAPTER 1: Introduction to ChIP-seq; 1.1 CHIP-SEQ EXPERIMENT; 1.2 IMPROVED DETECTION PROTOCOLS; 1.2.1 ChIP-exo; 1.2.2 ChIP-nexus; 1.2.3 CUT 1.2.4 DamID; 1.3 CHIP-SEQ DATA ANALYSIS WORKFLOW; 1.4 DESIGNING A CHIP-SEQ EXPERIMENT; 1.4.1 ChIP-seq controls; 1.4.2 Sources of bias; 1.4.3 Antibody quality; 1.4.4 Read depth; 1.4.5 Read properties; 1.4.6 Replicates; CHAPTER 2: Getting Started; 2.1 CHIP-SEQ DATASETS; 2.2 COMPUTATIONAL REQUIREMENTS; 2.2.1 Computing environment; 2.2.2 Data; 2.2.3 Software
2.2.4 File formats2.3 DATA RETRIEVAL FROM GEO; 2.4 CODING TIPS; 2.5 GRAPHICAL USER INTERFACE TOOLS; CHAPTER 3: General Quality Control; 3.1 INTRODUCTION; 3.1.1 FASTQ files; 3.1.2 Available tools; 3.2 MEASURES OF HTS DATA QUALITY; 3.2.1 Selected quality metrics; 3.2.2 FastQC; 3.3 TRIMMING AND FILTERING; 3.3.1 Adapter removal; 3.3.2 Low-quality trimming; 3.3.3 Trim Galore!; CHAPTER 4: Genomic Alignment; 4.1 INTRODUCTION; 4.1.1 Alignment concepts; 4.1.2 Available tools; 4.2 PARAMETERS AND CONSIDERATIONS; 4.2.1 Mismatches; 4.2.2 Multi-mapping; 4.2.3 Other parameters; 4.2.4 Output format
4.3 GENOMIC ALIGNMENT WITH BOWTIE 2CHAPTER 5: ChIP-seq-specific Quality Control; 5.1 CHIP-SEQ-SPECIFIC QUALITY METRICS; 5.1.1 Signal enrichment; 5.1.2 Forward and reverse read distribution; 5.1.3 Duplicate reads; 5.2 CHIPQC; CHAPTER 6: Peak Calling; 6.1 CHIP-SEQ SIGNAL TYPES; 6.1.1 Sharp signal for transcription factors; 6.1.2 Broad signal for histone marks; 6.1.3 Mixed signal for RNA polymerase II; 6.2 GENERAL PEAK CALLING STRATEGY; 6.2.1 Estimation of fragment size; 6.2.2 Enrichment of reads; 6.2.3 Significance score; 6.2.4 Multiple testing correction; 6.2.5 Choice of thresholds
6.3 EXISTING TOOLS AND CONSIDERATIONS6.3.1 Single-end versus paired-end libraries; 6.3.2 Sequencing depth and library complexity; 6.3.3 Experimental resolution; 6.3.4 New generation of peak callers; 6.3.5 Post-processing; 6.4 PEAKZILLA FOR TRANSCRIPTION FACTOR DATA; 6.5 MACS2 FOR HISTONE MARK DATA; 6.6 SATURATION ANALYSIS; CHAPTER 7: Data Visualisation; 7.1 READ DENSITIES; 7.2 PEAK REGIONS; 7.3 GENOME BROWSER; CHAPTER 8: Comparative Analysis; 8.1 OVERLAP OF PEAK REGIONS; 8.2 IRREPRODUCIBLE DISCOVERY RATE (IDR); 8.2.1 Peak calling for IDR; 8.2.2 Calculating IDR
8.3 COMPARISON OF READ DENSITIES8.3.1 Merging peak regions; 8.3.2 Counting reads for each sample; 8.3.3 Normalising read counts; 8.3.4 Comparing read counts; 8.4 DIFFERENTIAL BINDING ANALYSIS; 8.4.1 Using DESeq2; 8.4.2 DiffBind; CHAPTER 9: Downstream Analyses; 9.1 GENOMIC CONTEXT; 9.1.1 Genomic location; 9.1.2 Distance to genes; 9.2 FUNCTIONAL ANALYSES; 9.2.1 Assignment to target genes; 9.2.2 Gene ontology analysis; 9.2.3 Other gene-set enrichment analyses; 9.3 SEQUENCE ANALYSIS; 9.3.1 Motif analysis; 9.3.2 Sequence conservation; 9.4 INTEGRATION WITH OTHER DATASETS
Notes 9.4.1 Additional ChIP-seq datasets
Print version record
Form Electronic book
Author Zarnack, Kathi
Bardet, Anaïs F
ISBN 9780429946400
0429946406