과학 공학
Bioinformatics at the Bench
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| 듣기기능 | 미지원 | 파일정보 | |
|---|---|---|---|
| 총 용량 | 7.3 MB | 이용기기 | |
| ISBN | 9791139057157 | ||
책 소개
Welcome to the Dry Lab
Biology has changed. Ten years ago, the most important tool in the lab was the pipette. Today, it is the command line. This book is not a textbook; it is a laboratory manual. Just as you follow a protocol to run a Western Blot, you will follow the protocols in this book to analyze the human genome.
The "Black Box" Approach
Many students fear bioinformatics because they think they need to be computer scientists. You do not. You only need to understand the "Input -> Process -> Output" logic.
· Input: The biological data DNA sequences.
· Process: The tool The "Black Box" that does the math.
· Output: The biological answer A list of mutations or gene expression changes.
Your 16-Week Mission
Over the next semester, you will act as the lead bioinformatician for two major projects:
1. Weeks 1-9 Genomics: You will analyze the genome of a family trio Father, Mother, Daughter to find a genetic variant inherited by the daughter. You will handle raw DNA sequencing data just like a clinical geneticist.
2. Weeks 10-16 Transcriptomics: You will analyze RNA-seq data from human airway cells treated with a steroid drug. You will discover exactly which genes are turned on or off by the treatment.
No Coding Required
We will not be writing software. We will be using software. If you can type a sentence, you can finish this book. Open your terminal. Let's begin.
Biology has changed. Ten years ago, the most important tool in the lab was the pipette. Today, it is the command line. This book is not a textbook; it is a laboratory manual. Just as you follow a protocol to run a Western Blot, you will follow the protocols in this book to analyze the human genome.
The "Black Box" Approach
Many students fear bioinformatics because they think they need to be computer scientists. You do not. You only need to understand the "Input -> Process -> Output" logic.
· Input: The biological data DNA sequences.
· Process: The tool The "Black Box" that does the math.
· Output: The biological answer A list of mutations or gene expression changes.
Your 16-Week Mission
Over the next semester, you will act as the lead bioinformatician for two major projects:
1. Weeks 1-9 Genomics: You will analyze the genome of a family trio Father, Mother, Daughter to find a genetic variant inherited by the daughter. You will handle raw DNA sequencing data just like a clinical geneticist.
2. Weeks 10-16 Transcriptomics: You will analyze RNA-seq data from human airway cells treated with a steroid drug. You will discover exactly which genes are turned on or off by the treatment.
No Coding Required
We will not be writing software. We will be using software. If you can type a sentence, you can finish this book. Open your terminal. Let's begin.
목차
Part 1: The Lab Environment Weeks 1-2
Week 1 : The Terminal & The Heist
Introduction--7
Methods-----13
Results-------18
Discussion---20
Week 2 : RStudio & The Sample Sheet
Introduction--22
Methods------26
Results--------28
Discussion----30
Part 2 : Genomics Weeks 3-9
Week 3 : Quality Control QC
Introduction--32
Methods------35
Results--------38
Discussion----40
Week 4 : Trimming
Introduction--42
Methods------44
Results--------47
Discussion----49
Week 5 : Alignment Mapping
Introduction--51
Methods------54
Results--------56
Discussion----58
Week 6 : The Binary Conversion BAM
Introduction--60
Methods------65
Results--------68
Discussion----70
Week 7 : Variant Calling
Introduction--72
Methods------77
Results--------80
Discussion----82
Week 8 : Filtering
Introduction--84
Methods------86
Results--------89
Discussion----91
Week 9 : Validation IGV
Introduction--93
Methods------98
Results--------102
Discussion----104
Part 3: Transcriptomics Weeks 10-16
Week 10 : RNA Retrieval
Introduction--106
Methods------109
Results--------110
Discussion----112
Week 11 : Spliced Alignment
Introduction--114
Methods------116
Results--------118
Discussion----120
Week 12 : Counting Reads
Introduction--122
Methods------126
Results--------132
Discussion----134
Week 13 : Normalization RStudio
Introduction--136
Methods------141
Results--------146
Discussion----148
Week 14 : Differential Expression
Introduction--150
Methods------153
Results--------155
Discussion----157
Week 15 : The Volcano Plot
Introduction--159
Methods------166
Results--------170
Discussion----172
Week 16 : Heatmaps & Final Report
Introduction--174
Methods------176
Results--------178
Discussion----180
Reference-----174
Week 1 : The Terminal & The Heist
Introduction--7
Methods-----13
Results-------18
Discussion---20
Week 2 : RStudio & The Sample Sheet
Introduction--22
Methods------26
Results--------28
Discussion----30
Part 2 : Genomics Weeks 3-9
Week 3 : Quality Control QC
Introduction--32
Methods------35
Results--------38
Discussion----40
Week 4 : Trimming
Introduction--42
Methods------44
Results--------47
Discussion----49
Week 5 : Alignment Mapping
Introduction--51
Methods------54
Results--------56
Discussion----58
Week 6 : The Binary Conversion BAM
Introduction--60
Methods------65
Results--------68
Discussion----70
Week 7 : Variant Calling
Introduction--72
Methods------77
Results--------80
Discussion----82
Week 8 : Filtering
Introduction--84
Methods------86
Results--------89
Discussion----91
Week 9 : Validation IGV
Introduction--93
Methods------98
Results--------102
Discussion----104
Part 3: Transcriptomics Weeks 10-16
Week 10 : RNA Retrieval
Introduction--106
Methods------109
Results--------110
Discussion----112
Week 11 : Spliced Alignment
Introduction--114
Methods------116
Results--------118
Discussion----120
Week 12 : Counting Reads
Introduction--122
Methods------126
Results--------132
Discussion----134
Week 13 : Normalization RStudio
Introduction--136
Methods------141
Results--------146
Discussion----148
Week 14 : Differential Expression
Introduction--150
Methods------153
Results--------155
Discussion----157
Week 15 : The Volcano Plot
Introduction--159
Methods------166
Results--------170
Discussion----172
Week 16 : Heatmaps & Final Report
Introduction--174
Methods------176
Results--------178
Discussion----180
Reference-----174