Appendix IV. Teaching Materials

1) Teaching Files

[email protected] Cloud: Lu Lab Public Files/Bioinformatics Tutorial

2) Teaching Docker

[email protected] Cloud: Lu Lab Public Files/Bioinformatics Tutorial
    PART I + II + PART III.1-2 + PART III.6.1
      docker image name: bioinfo_PartI-PartII-PartIII1-3.tar.gz
      software installed: BLAST 2.6.0+; bowtie 1.0.0; samtools 1.7 (using htslib 1.7-2); TopHat v2.0.9; cufflinks v2.1.1; cuffmerge v2.1.1; cuffdiff v2.1.1; R 3.5.1; perl v5.26.1; Python 2.7; bamtools 1.0.2; java 1.8.0_181; rMATS-turbo-Linux-UCS4 v3.1.0; homer v4.10.3;
    PART II.4. Clinical Analysis - Survival Curve
      docker image name: bioinfo_roc_survival.tar.gz
      software installed: R 3.5.1; Python 2.7
    PART III.1.1 Paired-end mapping
      docker image name: bioinfo_pairend.tar.gz
      software installed: STAR:2.5.3a;
    PART III.1.2 bedtools and samtools
      docker image name: bioinfo_tool.tar.gz
      software installed: bedtools v2.25.0,samtools v1.11;
    PART III.2.1 Expression Matrix
      docker image name: bioinfo_tsinghua_featurecount.tar.gz
      software installed: featureCounts;
    PART III.4. Motif
      docker image name: bioinfo_motif.tar.gz
      software installed: R 3.5.1; meme 4.11.4; RNAfold 2.4.8; BEAM; RNApromo
    PART III.5. Network coexpression - Co-expression Network
      docker image name: bioinfo-coexp.tar.gz
      software installed: R 3.5.1 ; bedtools v2.27.1
    PART III.5. Network coexpression - miRNA target
      docker image name: bioinfo_mirna_target.tar.gz
      software installed: miRanda;psRobot: v1.2; miRanda: aug2010;
    PART III.5. Network coexpression - RBP-RNA Interactions
      docker image name: bioinfo_rbp.tar.gz
    PART III.6. RNA Regulation Analysis - RNA Editing
      docker image name: bioinfo_rnaeditor.tar.gz
      software installed: RNAEditor
    PART III.6. RNA Regulation Analysis - APA,Ribo-seq,Structure-seq
      docker image name: bioinfo_tsinghua_6.2_apa_6.3_ribo_6.4_structure.tar.gz
      software installed: perl v5.26.1; DaPars; Ribowave; R 3.5.1; bedtools v2.25.0; shapemapper
    PART III.6. RNA Regulation Analysis - Chimeric RNA
      docker image name: bioinfo.chimeric.tar.gz
      software installed: STAR-Fusion: 1.8.1;
    PART III.6. RNA Regulation Analysis - SNV
      docker image name: bioinfo_snv.tar.gz
      software installed: STAR: 2.7.1a; annovar:2018-04-16; GATK:4.1.3.0;
    PART III.6. RNA Regulation Analysis - CLIP-seq
      docker image name: bioinfo_clip_seq.tar.gz;

3) Teaching Singularity

[email protected] Cloud: Lu Lab Public Files/Bioinformatics Tutorial
    PART I + II + PART III.1-3
      Singularity image name: /data/images/bioinfo_tsinghua.simg
      software installed: BLAST 2.6.0+; bowtie 1.0.0; samtools 1.7 (using htslib 1.7-2); TopHat v2.0.9; cufflinks v2.1.1; cuffmerge v2.1.1; cuffdiff v2.1.1; R 3.5.1; perl v5.26.1; Python 2.7; bamtools 1.0.2; java 1.8.0_181; rMATS-turbo-Linux-UCS4 v3.1.0; homer v4.10.3;
    PART III.1.1 Paired-end mapping
      docker image name: /data/images/bioinfo_pairend.simg
      software installed: STAR:2.5.3a;
    PART III.1.2 bedtools and samtools
      docker image name: /data/images/bioinfo_tool.simg
      software installed: bedtools v2.25.0,samtools v1.11;
    PART III.4. Motif
      docker image name: /data/images/bioinfo_motif.simg
      software installed: R 3.5.1; meme 4.11.4; RNAfold 2.4.8; BEAM; RNApromo
    PART III.6. RNA Regulation Analysis - RNA Editing
      docker image name: /data/images/bioinfo_rnaeditor.simg
      software installed: RNAEditor
    PART III.6. RNA Regulation Analysis - APA,Ribo-seq,Structure-seq
      docker image name: /data/images/bioinfo_tsinghua_6.2_apa_6.3_ribo_6.4_structure.simg
      software installed: perl v5.26.1; DaPars; Ribowave; R 3.5.1; bedtools v2.25.0; shapemapper
    PART III.6. RNA Regulation Analysis - Chimeric RNA
      docker image name: /data/images/bioinfo_chimeric.simg
      software installed: STAR-Fusion: 1.8.1;

4) Teaching Videos

[email protected] Cloud: Lu Lab Public Files/Bioinformatics Tutorial

Part I. Basic Skills

Section
Content
Bilibili
Youtube
Tsinghua Cloud Location*
Narrated by
Getting Started
markdown
Getting Started/
internet
Getting Started
git&github
Getting Started/
internet
1.Setup - Docker
How to use docker
@Youtube
Setup/
GX
1.Setup - Cluster
How to use cluster - submit jobs
Setup/
LXF
2.Linux - Basic
Linux小白入门
Linux and Programming/
internet
2.Linux - Basic
Linux Editor -nano
Linux and Programming/
internet
2.Linux - Basic
How to use Linux (docs)
@Youtube
Linux and Programming/
ZJL
2.Linux - Basic
How to use Vim
Linux and Programming/
internet
2.Linux - Practice Guide
Programming in Linux
Linux and Programming/
LXF
2.Linux - Bash
Shell Script
Linux and Programming/
internet
3.R - Basics
R语言系统教程(25小节)
Linux and Programming/
internet
3.R - Basics
R语言基础教程(6讲)
@Youtube
Linux and Programming/
internet
3.R - Basics
How to use R
@Youtube
Linux and Programming/
ZJL
3.R - plot
R plot - ggplot2
@bilibili
@Youtube
Linux and Programming/
internet

Part II. Basic Analyses

Section
Content
Bilibili
Youtube
Tsinghua Cloud Location*
Narrated by
1.Blast
Blast
Basic Analysis/
LXF
2.Conservation Analysis
Conservation Analysis
Basic Analysis/
LXF
3.Function Analysis
GO&KEGG
Basic Analysis/
LXF
3.Function Analysis
GSEA
Basic Analysis/
internet

Part III. NGS Data Analyses

Section
Content
Bilibili
Youtube
Tsinghua Cloud Location*
Narrated by
0.seq tech.
Sequencing Technologies
Sequencing Technologies/ (link)
internet
1.mapping
Mapping
NGS Analysis/
YHT
1.mapping
Genome Browser: IGV
@Youtube
NGS Analysis/
ZYX
1.mapping
Genome Browser: UCSC
@Youtube
NGS Analysis/
ZYX
2.RNA-seq
Differential Expression
NGS Analysis/
YHT
2.RNA-seq
Alternative Splicing
NGS Analysis/
LXF
3.ChIP-seq
ChIP-seq Analysis
NGS Analysis/
ZS
4.Motif
Motif Analysis
NGS Analysis/
LXF
5.Network
Co-expression Network
NGS Analysis/
internet
5.Network
miRNA Targets
NGS Analysis/
internet
5.Network
RBP-RNA Interactions
NGS Analysis/
internet
Last modified 29d ago