Exercise - nibb-gitc/gitc2025mar-rnaseq GitHub Wiki

演習問題

NGSの基礎 1, 2

• ex101 -- NGS基礎問題集
• ex201 -- IGVによる可視化 RNA-Seq結果の可視化
• ex202 -- IGVによる可視化（特別編SARS-CoV-2）
• ex203 -- IGVによる可視化 batch処理
• ex204 -- IGVによる可視化 メチル化callingデータの可視化

RNA-seq基礎 3

• ex301 -- data import and visualization
• ex302 -- MA plot
• ex303 -- Volcano plot

RNA-seq解析パイプライン transcript-based (4) and genome-based (5) pipeline

• ex401 -- Transcript-based RNA-seq pipeline: mapping-free pipeline using Salmon
• ex402.v2 -- edgeR: Differential expression analysis (classic) [updated]
• ex403.v2 -- [advanced] edgeR (linear model) [updated]
• ex501 -- Genome-based RNA-seq pipeline (mapping and counting)

多変量解析 6

• ex601 -- 階層クラスタリング、PCA
• ex602 -- MDSによる可視化
• ex603 -- k-means法による次元圧縮
• ex604 -- t-SNE, UMAP

RNA-seq解析パイプライン de novo 7

• ex701 -- Trinity de novo assembly
• ex702 -- BUSCO 練習
• ex703 -- BUSCO によるtranscritomeの評価

アノテーションやGene Ontology解析 8

• ex801 -- Annotation using similarity based methods
• ex802 -- GO enrichment analysis (with public annotation)
• ex803 -- GO enrichment analysis (with user annotation)

実戦演習

• case1 -- transcript-based RNA-seq, pair-wise comparison. (salmon/edgeR )
• case2_renew -- genome-based RNA-seq analysis (Cutadapt/HISAT2/StringTie/edgeR workflow)
• case3 -- transcript-based RNA-seq, multivariate analysis of three samples including clustering (salmon/edgeR ) [updated]
• case4 -- Annotate Trinity assembly using BLAST