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
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