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
ssh and ssh keys
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:
Basics
Pre-processing, Mapping, Annotation and QC.
Expression Matrix
Differential Expression Analysis and Clustering
Advanced
Normalization
Imputation
Control Data
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)
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
fasta
fastaq
gff/gtf
bam
bed
bigwig
Shared dirs/data:
~/genomes/human_hg38
sequences/ #sequences of reference genome (fasta format)
index/ # indexed genome sequences
gtf/ #annotation of reference genome
Make your own project dir:
d) Get the software ready
Install bioinformatics software in Linux (centos)
Video
a) Introduction exRNA-seq
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