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
Download Link for Docker images
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
Download Link for Singularity images
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
Link of 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