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RNA-Seq.yml
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RNA-Seq.yml
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name: "RNA-Seq"
type: "use"
title: "RNA-Seq data analysis"
summary: "RNA-sequencing is a method used to reveal the presence and quantity of RNA in a biological sample at a given moment in time."
docker_image: "bgruening/galaxy-rna-seq-training"
requirements:
-
title: "Galaxy introduction"
type: "internal"
link: "/Introduction/"
-
title: "Quality control"
type: "internal"
link: "/NGS-QC"
material:
-
title: "Introduction"
type: "introduction"
slides: "yes"
-
title: "Reference-based RNA-seq data analysis"
type: "tutorial"
name: "ref_based"
zenodo_link: "https://zenodo.org/record/290221"
galaxy_tour: "ref_based_rna_seq"
hands_on: "yes"
slides: "no"
questions:
- "What are the effects of Pasilla (PS) gene depletion on splicing events?"
- "How to analyze RNA sequencing data using a reference genome?"
objectives:
- "Analysis of RNA sequencing data using a reference genome"
- "Analysis of differentially expressed genes"
- "Identification of functional enrichment among differentially expressed genes"
time_estimation: "1d"
key_points:
- "Using a spliced mapping tool for eukaryotic RNA seq data"
- "Running a differential gene expression with taking care of the factors to study"
- "Running a differential exon usage with taking care of the factors to stud"
requirements:
-
title: "Mapping"
type: "internal"
link: "/NGS-mapping"
-
title: "IGV"
type: "internal"
link: "/Introduction/IGV"
-
title: "De novo transcriptome reconstruction with RNA-seq"
type: "tutorial"
name: "de_novo"
zenodo_link: "https://zenodo.org/record/254485#.WKODmRIrKRu"
galaxy_tour: "..."
hands_on: "yes"
slides: "no"
questions:
- "What genes are differentially expressed between G1E cells and megakaryocytes?"
- "How can we generate a transcriptome de novo from RNA sequencing data?"
objectives:
- "Analysis of RNA sequencing data using a reference genome"
- "Reconstruction of transcripts without reference transcriptome (de novo)"
- "Analysis of differentially expressed genes"
time_estimation: "6h"
key_points:
- "Simple sentence to sum up the first key point of the tutorial (Take home message)"
- "Second key point"
- "Third key point"
- "..."
requirements:
-
title: "Mapping"
type: "internal"
link: "/NGS-mapping"
-
title: "Trackster"
type: "external"
link: "https://wiki.galaxyproject.org/Learn/Visualization"
maintainers:
-
name: "Bérénice Batut"
github_username: "bebatut"
email: "[email protected]"
-
name: "Maintainer 2"
github_username: "maintainer2"
email: "[email protected]"
contributors:
-
name: "Bérénice Batut"
github_username: "bebatut"
email: "[email protected]"
-
name: "Mallory Freeberg"
github_username: "malloryfreeberg"
email: "[email protected]"
-
name: "Mo Heydarian"
github_username: "MoHeydarian"
email: "[email protected]"
references:
-
authors: "Shirley Pepke et al"
title: "Computation for ChIP-seq and RNA-seq studies"
link: "http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1371.html"
summary: ""
-
authors: "Paul L. Auer & R. W. Doerge"
title: "Statistical Design and Analysis of RNA Sequencing Data"
link: "http://www.genetics.org/content/185/2/405"
summary: "Insights into proper planning of your RNA-seq run! To read before any RNA-seq experiment!"
-
authors: "Ian Korf"
title: "Genomics: the state of the art in RNA-seq analysis"
link: "http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2735.html"
summary: "A refreshingly honest view on the non-trivial aspects of RNA-seq analysis"
-
authors: "Marie-Agnès Dillies et al"
title: "A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis"
link: "http://bib.oxfordjournals.org/content/14/6/671"
summary: "Systematic comparison of seven representative normalization methods for the differential analysis of RNA-seq data (Total Count, Upper Quartile, Median (Med), DESeq, edgeR, Quantile and Reads Per Kilobase per Million mapped reads (RPKM) normalization)"
-
authors: "Franck Rapaport et al"
title: "Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data"
link: "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-9-r95"
summary: "Evaluation of methods for differential gene expression analysis"
-
authors: "Charlotte Soneson & Mauro Delorenzi"
title: "A comparison of methods for differential expression analysis of RNA-seq data"
link: "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-91"
summary: ""
-
authors: "Adam Roberts et al"
title: "Improving RNA-Seq expression estimates by correcting for fragment bias"
link: "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-3-r2"
summary: ""
-
authors: "Manuel Garber et al"
title: "Computational methods for transcriptome annotation and quantification using RNA-seq"
link: "http://www.nature.com/nmeth/journal/v8/n6/abs/nmeth.1613.html"
summary: "Classical paper about the computational aspects of RNA-seq data analysis"