├── README.md ├── Tutorial.md ├── Tutorial.pdf ├── ext └── meta_additional.tsv └── img ├── GUI_vs_CLI.jpg ├── PuTTY.png ├── axolotl.png ├── boxplot_DEG_hcl.png ├── boxplot_DEG_hcl_reordered.png ├── boxplot_DEG_maxlayer.png ├── david_c2.png ├── david_start.png ├── exon_skipping.png ├── fastqc.png ├── gsea_L4_hnbml5.png ├── hcl_DEG.png ├── hcl_combat_meta.png ├── hcl_expressed.png ├── hcl_expressed_meta.png ├── hcl_highvar_meta.png ├── heatmap_DEG_clustered_viridis.png ├── heatmap_DEG_default.png ├── heatmap_DEG_viridis.png ├── hist_avg_expr_base.png ├── hist_avg_expr_ggplot.png ├── hist_num_det.png ├── kallisto.jpg ├── layer_deconvolution.png ├── new_r_script.png ├── pca_eigs.png ├── pca_x.png ├── pca_x_combat.png ├── pca_x_highvar.png ├── r-color-palettes-r-color-scales.png ├── rstudio.png ├── rstudio_server_login.png ├── run_selector_1.png ├── run_selector_2.png ├── run_selector_3.png ├── run_selector_4.png ├── scatter_ancova_DESeq2.png ├── ssh.png ├── star_seed_search.jpeg ├── ucsc_genome_browser.png ├── volcano_ancova.png └── volcanoplot_example.png /README.md: -------------------------------------------------------------------------------- 1 | # Tutorial for RNA-seq data preprocessing and analysis 2 | This tutorial is made for the Master lecture "Introduction to Genomics" at D-BSSE, ETH Zurich. In this tutorial, a walk-through guideline is provided to lead people that are new to RNA-seq data analysis through their first analysis of an RNA-seq data set. The tutorial also includes some very basic introduction of the command line interface of the Linux system, which is heavily used when going through the pipeline. 3 | 4 | The example data set presented in the tutorial is a subset of the RNA-seq data in the paper "Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques" published in Nature Neuroscience in 2017." 5 | -------------------------------------------------------------------------------- /Tutorial.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quadbio/RNAseq_tutorial/d4f4d49b5641da7693c1dacdf4b7697234613555/Tutorial.pdf -------------------------------------------------------------------------------- /ext/meta_additional.tsv: -------------------------------------------------------------------------------- 1 | Individual Sample Layer 2 | DS1_H1 DS1_H1_01 L1 3 | DS1_H1 DS1_H1_03 L2 4 | DS1_H1 DS1_H1_06 L3 5 | DS1_H1 DS1_H1_07 L4 6 | DS1_H1 DS1_H1_10 L5 7 | DS1_H1 DS1_H1_13 L6 8 | DS1_H1 DS1_H1_18 WM 9 | DS1_H2 DS1_H2_01 L1 10 | DS1_H2 DS1_H2_02 L2 11 | DS1_H2 DS1_H2_06 L3 12 | DS1_H2 DS1_H2_08 L4 13 | DS1_H2 DS1_H2_11 L5 14 | DS1_H2 DS1_H2_14 L6 15 | DS1_H2 DS1_H2_18 WM 16 | DS1_H3 DS1_H3_02 L2 17 | DS1_H3 DS1_H3_05 L3 18 | DS1_H3 DS1_H3_06 L4 19 | DS1_H3 DS1_H3_10 L5 20 | DS1_H3 DS1_H3_13 L6 21 | DS1_H3 DS1_H3_18 WM 22 | DS1_H4 DS1_H4_03 L3 23 | DS1_H4 DS1_H4_06 L4 24 | DS1_H4 DS1_H4_09 L5 25 | DS1_H4 DS1_H4_12 L6 26 | DS1_H4 DS1_H4_18 WM 27 | -------------------------------------------------------------------------------- /img/GUI_vs_CLI.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quadbio/RNAseq_tutorial/d4f4d49b5641da7693c1dacdf4b7697234613555/img/GUI_vs_CLI.jpg -------------------------------------------------------------------------------- /img/PuTTY.png: 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