Muutke küpsiste eelistusi

E-raamat: Practical Guide to ChIP-seq Data Analysis

4.00/5 (2 hinnangut Goodreads-ist)
(Queen Mary University London, UK), , (Goethe University, Frankfurt, Germany)
Teised raamatud teemal:
  • Formaat - PDF+DRM
  • Hind: 24,69 €*
  • * hind on lõplik, st. muud allahindlused enam ei rakendu
  • Lisa ostukorvi
  • Lisa soovinimekirja
  • See e-raamat on mõeldud ainult isiklikuks kasutamiseks. E-raamatuid ei saa tagastada.
Practical Guide to ChIP-seq Data AnalysisSuurem pilt
Teised raamatud teemal:

DRM piirangud

  • Kopeerimine (copy/paste):

    ei ole lubatud

  • Printimine:

    ei ole lubatud

  • Kasutamine:

    Digitaalõiguste kaitse (DRM)
    Kirjastus on väljastanud selle e-raamatu krüpteeritud kujul, mis tähendab, et selle lugemiseks peate installeerima spetsiaalse tarkvara. Samuti peate looma endale  Adobe ID Rohkem infot siin. E-raamatut saab lugeda 1 kasutaja ning alla laadida kuni 6'de seadmesse (kõik autoriseeritud sama Adobe ID-ga).

    Vajalik tarkvara
    Mobiilsetes seadmetes (telefon või tahvelarvuti) lugemiseks peate installeerima selle tasuta rakenduse: PocketBook Reader (iOS / Android)

    PC või Mac seadmes lugemiseks peate installima Adobe Digital Editionsi (Seeon tasuta rakendus spetsiaalselt e-raamatute lugemiseks. Seda ei tohi segamini ajada Adober Reader'iga, mis tõenäoliselt on juba teie arvutisse installeeritud )

    Seda e-raamatut ei saa lugeda Amazon Kindle's. 

Chromatin immunoprecipitation sequencing (ChIP-seq), which maps the genome-wide localization patterns of transcription factors and epigenetic marks, is among the most widely used methods in molecular biology. Practical Guide to ChIP-seq Data Analysis will guide readers through the steps of ChIP-seq analysis: from quality control, through peak calling, to downstream analyses. It will help experimental biologists to design their ChIP-seq experiments with the analysis in mind, and to perform the basic analysis steps themselves. It also aims to support bioinformaticians to understand how the data is generated, what the sources of biases are, and which methods are appropriate for different analyses.

Arvustused

I found the book to be very well structured; the topic is presented following a logical progression, guiding the reader through a ChIP-seq experiment, illustrating each step of the analytical workflow. The workflow is nicely divided in smaller blocks, each including the relevant theory and practical exercises (consisting of code) that enable the reader to put the theory intro practice, plus suggestions for additional reading.

I particularly appreciated the reference to biases and important issues that need to be considered when planning an experiment, as well as the discussion of data quality issues, extremely relevant to users dealing with publicly available data.

This will be a great resource for teaching, particularly given the use of public data as well as open source software. All that is presented in the book is reproducible, making it an extremely useful resource for any learner. I also appreciated the chapter dedicated to downstream analysis and interpretation great to see as extremely useful and not often covered to the extent required; similar observation for the integration with other data types, a very timely subject of great interest to many researchers working with different data types and in need of combining the results of different experiment types. This book will be useful to different audiences (experimentalists as well as bioinformaticians) and it is written in a way which is easy to understand for non-technical audiences.

-Gabriella Rustici, University of Cambridge

Chapter 1 Introduction to ChIP-seq
1(10)
Borbala Mifsud
1.1 Chip-Seq Experiment
1(3)
1.2 Improved Detection Protocols
4(1)
1.2.1 ChIP-exo
4(1)
1.2.2 ChIP-nexus
4(1)
1.2.3 CUT&RUN
4(1)
1.2.4 DamID
5(1)
1.3 Chip-Seq Data Analysis Workflow
5(1)
1.4 Designing A Chip-Seq Experiment
6(5)
1.4.1 ChIP-seq controls
6(1)
1.4.2 Sources of bias
6(1)
1.4.3 Antibody quality
7(1)
1.4.4 Read depth
8(1)
1.4.5 Read properties
8(1)
1.4.6 Replicates
9(2)
Chapter 2 Getting Started
11(10)
Anais Bardet
2.1 Chip-Seq Datasets
11(2)
2.2 Computational Requirements
13(2)
2.2.1 Computing environment
13(1)
2.2.2 Data
13(1)
2.2.3 Software
14(1)
2.2.4 File formats
15(1)
2.3 Data Retrieval From Geo
15(1)
2.4 Coding Tips
16(3)
2.5 Graphical User Interface Tools
19(2)
Chapter 3 General Quality Control
21(6)
Kathi Zarnack
3.1 Introduction
21(1)
3.1.1 FASTQ files
21(1)
3.1.2 Available tools
22(1)
3.2 Measures Of HTS Data Quality
22(3)
3.2.1 Selected quality metrics
22(3)
3.2.2 FastQC
25(1)
3.3 Trimming And Filtering
25(2)
3.3.1 Adapter removal
25(1)
3.3.2 Low-quality trimming
26(1)
3.3.3 Trim Galore!
26(1)
Chapter 4 Genomic Alignment
27(8)
Kathi Zarnack
4.1 Introduction
27(1)
4.1.1 Alignment concepts
27(1)
4.1.2 Available tools
28(1)
4.2 Parameters And Considerations
28(3)
4.2.1 Mismatches
28(1)
4.2.2 Multi-mapping
29(1)
4.2.3 Other parameters
29(2)
4.2.4 Output format
31(1)
4.3 Genomic Alignment With Bowtie 2
31(4)
Chapter 5 ChIP-seq-specific Quality Control
35(6)
Borbala Mifsud
5.1 Chip-Seq-Specific Quality Metrics
35(4)
5.1.1 Signal enrichment
35(3)
5.1.2 Forward and reverse read distribution
38(1)
5.1.3 Duplicate reads
38(1)
5.2 Chipqc
39(2)
Chapter 6 Peak Calling
41(12)
Anais Bardet
6.1 Chip-Seq Signal Types
41(1)
6.1.1 Sharp signal for transcription factors
41(1)
6.1.2 Broad signal for histone marks
42(1)
6.1.3 Mixed signal for RNA polymerase II
42(1)
6.2 General Peak Calling Strategy
42(3)
6.2.1 Estimation of fragment size
42(2)
6.2.2 Enrichment of reads
44(1)
6.2.3 Significance score
44(1)
6.2.4 Multiple testing correction
44(1)
6.2.5 Choice of thresholds
44(1)
6.3 Existing Tools And Considerations
45(2)
6.3.1 Single-end versus paired-end libraries
45(1)
6.3.2 Sequencing depth and library complexity
46(1)
6.3.3 Experimental resolution
46(1)
6.3.4 New generation of peak callers
47(1)
6.3.5 Post-processing
47(1)
6.4 Peakzilla For Transcription Factor Data
47(2)
6.5 MACS2 For Histone Mark Data
49(1)
6.6 Saturation Analysis
50(3)
Chapter 7 Data Visualisation
53(6)
Anais Bardet
7.1 Read Densities
53(4)
7.2 Peak Regions
57(1)
7.3 Genome Browser
57(2)
Chapter 8 Comparative Analysis
59(18)
Anais Bardet
Borbala Mifsud
8.1 Overlap Of Peak Regions
59(2)
8.2 Irreproducible Discovery Rate (IDR)
61(3)
8.2.1 Peak calling for IDR
63(1)
8.2.2 Calculating IDR
64(1)
8.3 Comparison Of Read Densities
64(6)
8.3.1 Merging peak regions
65(1)
8.3.2 Counting reads for each sample
66(1)
8.3.3 Normalising read counts
66(1)
8.3.4 Comparing read counts
67(3)
8.4 Differential Binding Analysis
70(7)
8.4.1 Using DESeq2
70(3)
8.4.2 DiffBind
73(4)
Chapter 9 Downstream Analyses
77(16)
Anais Bardet
Kathi Zarnack
9.1 Genomic Context
77(6)
9.1.1 Genomic location
77(3)
9.1.2 Distance to genes
80(3)
9.2 Functional Analyses
83(2)
9.2.1 Assignment to target genes
83(1)
9.2.2 Gene ontology analysis
83(1)
9.2.3 Other gene-set enrichment analyses
84(1)
9.3 Sequence Analysis
85(4)
9.3.1 Motif analysis
85(2)
9.3.2 Sequence conservation
87(2)
9.4 Integration With Other Datasets
89(4)
9.4.1 Additional ChIP-seq datasets
89(2)
9.4.2 Expression data
91(1)
9.4.3 Other types of data
92(1)
Bibliography 93(6)
Index 99
Borbala Mifsud is an assistant professor in Epigenomics at the Hamad Bin Khalifa University, Doha, Qatar. She is a computational biologist with a background in molecular biology and works on 3D chromatin conformation and the integration of epigenomic data.

Kathi Zarnack is a principal investigator in Computational RNA Biology at the Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Germany. She is a computational biologist with a background in molecular biology and broad experience in analysing high-throughput sequencing data.

Anaïs F Bardet is a tenured researcher at the National Center for Scientific Research (CNRS) at the University of Strasbourg, France. She is a computational biologist and develops projects exploring the regulation of transcription factor binding.
Lisainfo e-raamatute kohta Lisainfo e-raamatute kohta
Püsilink: https://www.kriso.ee/db/97804299464002e.html
Märksõnad: