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NGS for natural scientist
  • 1. Preface
    • How to use this book
    • Motivation
    • Genomic data science as a tool to biologist
    • Next Generation Science (also NGS)
  • 2. Getting started
    • A step by step pipeline tutorial
    • Sequencing chemistry explained by Illumina
    • Joining a course
    • RNA quality and Library prep
    • (optional) My click moment about "Why Linux"
  • 3. Good-to-know beforehand
    • Experiment design
    • Single-end and Paired-end
    • Read per sample and data size
    • Normalization - RPKM/FPKM/TPM
    • Gene annotation
  • 4. Setting up terminal
    • My Linux terminal
    • Linux environment
    • R and RStudio
    • PATH
  • 5. FASTQ and quality control
    • Getting FASTQ files from online database
    • FASTQ quality assessment
  • 6. Mapping/alignment and quantification
    • Salmon
    • DESeq2
  • 7. Visualization
  • 8. Single cell RNA-Seq
  • 9. AWS cloud and Machine Learning
    • Machine Learning in a nutshell
    • R vs Python
    • Setting up ML terminal
    • Data exploration
  • (pending material)
    • graphPad
    • readings for ML
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  1. 1. Preface

Genomic data science as a tool to biologist

A concept that I believe to crack the bottle neck of connecting NGS and conventional science

PreviousMotivationNextNext Generation Science (also NGS)

Last updated 1 year ago

I believe that science is all about hypothesis testing. But the hypothesis that I am talking about here is a bit different from the way statisticians would like to put. For example,

Wait a second, what's the deal here? They could be essentially the same at some level. So the criticality lies in how to validate the conclusion. For the former I might want to perform any sort of quantifiable PCR to validate the expression, but for the latter I would like to see what if I use other treatment and what if I assess at different molecular level such as protein and/or other clinically/physiologically related phenotype.

The way you phrase your hypothesis dictates your research directions and methods, and thus output.

I am not saying who is better than who, I am saying that we should all work together. In my journey of self-educating to use the NGS tools, Mathematicians tends to create new terminology to suit their needs on some well-known "things", such as the "summarizing transcriptome to gene level" conversion used widely in DESeq2 related discussion. So sometimes I am also confused, in which line of professions or methodology that I am using to solve a natural science question which is universal to every single living things on the Earth. I mean, should I even need to worry about that when if we all are heading to the same Rome?