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:
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cd #go to my home
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ln -s /BioII/lulab_b/shared/genomes . #shared reference genome sequeunces and annotations
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ln -s /BioII/lulab_b/shared/shared_scripts . #shared scripts in Lu Lab
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ln -s /BioII/lulab_b/shared/projects/exRNA shared_exRNA_projects #shared projects' files
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    ~/genomes/human_hg38
      sequences/ #sequences of reference genome (fasta format)
      index/ # indexed genome sequences
      gtf/ #annotation of reference genome
Make your own project dir:
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cd # go to my home
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vim .bashrc # see my example in /home/john/.bashrc (and /home/john/shortcuts)
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mkdir github
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mkdir -p ~/projects/exRNA
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cd ~/projects/exRNA
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alias mkpr="mkdir -p {data/mapped,scripts,analysis}" # you can put this in your ~/.bashrc
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mkpr
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d) Get the software ready

Video

@Youtube
@Bilibili

Other pipelines for RNA-seq analyses

We also recommend some other Tutorials/Pipelines you can learn from:
Last modified 2yr ago