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 Docker images in the Files needed

• 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 Singularity images in the Files needed

• 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

See Videos in the Files needed