Introduction of PART II

写在前面的话

我们将通过实际的例子,也就是Case Study,来进行生物信息分析的教学和训练。这样的学习更加有目的性,也更加有趣,但是不足的地方是教学的内容会不够完备。

Work with a computing server remotely

  1. ssh and ssh keys

  2. nohub, screen or tmux

More Reading

<<Bioinformatics Data Skills>>

4) Working with Remote Machines

Let's start a real case

Identify novel exRNA biomarkers for cancer diagnosis

Outline:

  1. Basics

    1. Pre-processing, Mapping, Annotation and QC.

    2. Expression Matrix

    3. Differential Expression Analysis and Clustering

  2. Advanced

    1. Normalization

    2. Imputation

    3. Control Data

    4. Extension

a) Background Introduction

  • PPT: 0. Introduction of exRNA-seq.pdf (view on-line only, not downloadable)

  • Teaching Video: Week V - Part II. 0. Intr to exRNA-seq.mov

b) Understand your data

Type of RNA-seq

  • Default: (whole cell poly-A) RNA-seq (>200nt)

  • Other types:

    • small RNA-seq (<50nt)

    • total RNA-seq (ribosome removed) (>200nt)

    • nonpolyA RNA-seq (ribosome removed) (>200nt)

  • Different cell localizations:

    • nuc. (total)

    • chromosome (total)

    • cyto. (poly-A)

  • Single cell RNA-seq

  • exRNA-seq

    • cell free/MV/exosome/RNP

    • small/long

So what RNA-seq we are mapping and analyzing?

  • Sequencing machine ?

  • Single-strand V.S. Paired-end ?

  • Strand specific ?

  • Size selection ?

  • Poly-A enriched or total (ribosome removed) ?

  • Cellular localization ?

c) Organize your data

Data format:

  • fasta

  • fastaq

  • gff/gtf

  • bam

  • bed

  • bigwig

Shared dirs/data:

cd #go to my home
ln -s /BioII/lulab_b/shared/genomes . #shared reference genome sequeunces and annotations
ln -s /BioII/lulab_b/shared/shared_scripts . #shared scripts in Lu Lab
ln -s /BioII/lulab_b/shared/projects/exRNA shared_exRNA_projects #shared projects' files
  • ~/genomes/human_hg38

    • sequences/ #sequences of reference genome (fasta format)

    • index/ # indexed genome sequences

    • gtf/ #annotation of reference genome

Make your own project dir:

cd # go to my home
vim .bashrc # see my example in /home/john/.bashrc (and /home/john/shortcuts)
mkdir github
mkdir -p ~/projects/exRNA
cd ~/projects/exRNA
alias mkpr="mkdir -p {data/mapped,scripts,analysis}" # you can put this in your ~/.bashrc
mkpr

d) Get the software ready

Install bioinformatics software in Linux (centos)

Video

a) Introduction exRNA-seq

@Youtube

@Bilibili