Bioinformatics Tutorial - Basic
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Bioinformatics Tutorial - Basic
Getting Started
Part I. Basic Skills
1.Setup
2.Linux
3.R
4.Python
PART II. BASIC ANALYSES
1.Blast
2.Conservation Analysis
3.Function Analysis
4.Clinical Analyses
Part III. NGS DATA ANALYSES
1.Mapping
2.RNA-seq
3.ChIP-seq
4.Motif
5.Network
6.RNA Regulation Analyses
Part IV. MACHINE LEARNING
1.Machine Learning Basics
2.Machine Learning with R
3.Machine Learning with Python
Part V. Quiz
1.Precision Medicine - exSEEK
2.RNA Regulation - RiboShape
Appendix
Appendix I. Keep Learning
Appendix II. Databases & Servers
Appendix III. How to Backup
Appendix IV. Teaching Materials
Appendix V. Software and Tools
Appendix VI. Genome Annotations
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Appendix IV. Teaching Materials

1) Teaching Files

​Files needed by this Tutorial, including
  • Raw files needed for homework and practicing
  • Images of Docker and Singularity
  • Videos
  • PDFs of text books and education papers
  • ...

2) Teaching Docker

  • 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

  • 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

Appendix - Previous
Appendix III. How to Backup
Next - Appendix
Appendix V. Software and Tools
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Outline
1) Teaching Files
2) Teaching Docker
3) Teaching Singularity
4) Teaching Videos