Exercise - nibb-gitc/gitc2023mar-rnaseq GitHub Wiki

演習問題

NGSの基礎 1, 2

• ex101 -- NGS基礎問題集 [Nishide]
• ex201 -- IGVによる可視化 [Yamaguchi]
• ex202 -- IGVによる可視化（特別編SARS-CoV-2） [Shigenobu]

RNA-seq基礎 3

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

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 [shige]
• ex402 -- edgeR: Differential expression analysis (classic) [shige]
• ex403 -- [advanced] edgeR (linear model) [shige]
• ex501 -- Genome-based RNA-seq pipeline (mapping and counting) [Yamaguchi]

多変量解析 6

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

RNA-seq解析パイプライン de novo 7

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

アノテーションやGene Ontology解析 8

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

実戦演習

• case1 -- transcript-based RNA-seq, pair-wise comparison. (salmon/edgeR ) [shige]
• case2 -- genome-based RNA-seq analysis (HISAT2/StringTie/edgeR workflow) [Yamaguchi]
• case3 -- transcript-based RNA-seq, multivariate analysis of three samples including clustering (salmon/edgeR ) [shige]
• case4 -- Annotate Trinity assembly using BLAST [shige]

演習　特別編　SARS-CoV-2

• ex202 -- IGVによる可視化（SARS-CoV-2） [Shigenobu]