# Appendix IV. Teaching Materials

## 1) Teaching Files <a href="#teaching-files" id="teaching-files"></a>

[**Files needed** ](https://courses.ncrnalab.org/files)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 <a href="#teaching-docker" id="teaching-docker"></a>

**Download Docker images in the** [**Files needed** ](https://courses.ncrnalab.org/files)

* **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 <a href="#teaching-singularity" id="teaching-singularity"></a>

**Download Singularity images in the** [**Files needed** ](https://courses.ncrnalab.org/files)

* **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** ](https://courses.ncrnalab.org/files)


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