3. Good-to-know beforehand

It is an ordained ordeal.

Here I will list out what you should expect if you read this book in order. This checklist is also my own basic workflow whenever I start something new.

• Setting up hypothesis - both biological and statistical

• Experiment - to prepare for cell, tissue or animal samples

• Routine chunk

  • DNA/RNA extraction and purification - commercial kit would do

  • library preparation - commercial kit or sub-contract

  • sequencing run/fetching data from SRA/GEO

  • (if you obtained data from SRA/GEO) fastq dump

  • Quality control

  • (optional) trim adapters and clean up

  • alignment against a reference genome (or De Novo alignment)

  • assemble to get counts

• Data analysis - real fun starts from here

  • PCA plot

  • Heatmap

  • Gene Set Enrichment Analysis, or pathway analysis

• Hypothesis refinement - This is where natural science kick in again

• Experiment - a new round of journey

Keep reading on to make sense of this check list.