Case Study 1. exRNA-seq
Basic analyses for exRNA-seq
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
Other pipelines for RNA-seq analyses
We also recommend some other Tutorials/Pipelines you can learn from:
RNA-seq analysis pipeline:: https://github.com/mgonzalezporta/TeachingMaterial
lncRNA analysis pipeline: http://webhome.weizmann.ac.il/home/igoru/PLAR/
ENCODE pipelines: https://www.encodeproject.org/pipelines/
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