Nicolas Delhomme and Bastian Schiffthaler
This merely lists the various courses at which we taught RNA-Seq data
Scientific topics: RNA-Seq
Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Nicolas Delhomme and Bastian Schiffthaler
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/README.md
http://tess.elixir-uk.org/materials/nicolas-delhomme-and-bastian-schiffthaler
This merely lists the various courses at which we taught RNA-Seq data
@delhomme
@bastian
RNA-Seq
FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Expression estimation
This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed.
Scientific topics: RNA-Seq
Keywords: GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation
Expression estimation
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014/05_EMBO-October-2014-Expression-estimation.md
http://tess.elixir-uk.org/materials/expression-estimation
This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
RNA-Seq
GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation
Tutorial
This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.
Scientific topics: RNA-Seq
Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming
Tutorial
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014/00_EMBO-October-2014-Tutorial.md
http://tess.elixir-uk.org/materials/tutorial
This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
RNA-Seq
FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming
Populus tremula shows no evidence of sexual dimorphism
**Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and...
Scientific topics: RNA-Seq
Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression
Populus tremula shows no evidence of sexual dimorphism
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md
http://tess.elixir-uk.org/materials/populus-tremula-shows-no-evidence-of-sexual-dimorphism
**Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. The establishment of such sexual dimorphism would result in changes in gene expression patterns in non-floral organs.
Nicolas Delhomme @delhomme
Robinson K.
Mähler N.
Bastian Schiffthaler @bastian
Oenskog J.
Albrectsen B.
Ingvarsson P. K.
Hvidsten T. R.
Jansson S.
Street N. R.
RNA-Seq
FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression
Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material
Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and...
Scientific topics: RNA-Seq
Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014.md
http://tess.elixir-uk.org/materials/nicolas-delhomme-bastian-schiffthaler-october-2014-embo-course-material
Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and reproduces the Differential Expression analysis conducted in Robinson, Delhomme et al., 2014.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
RNA-Seq
FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Alignment
Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales.
Scientific topics: RNA-Seq
Keywords: BAM, Populus-tremula, RNA-Seq, QC, Alignment
Alignment
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014/03_EMBO-October-2014-Alignment.md
http://tess.elixir-uk.org/materials/alignment
Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
RNA-Seq
BAM, Populus-tremula, RNA-Seq, QC, Alignment
Annotation
This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses.
Scientific topics: RNA-Seq
Keywords: GFF3, Populus-tremula, RNA-Seq, Annotation
Annotation
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014/04_EMBO-October-2014-Annotation.md
http://tess.elixir-uk.org/materials/annotation
This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
RNA-Seq
GFF3, Populus-tremula, RNA-Seq, Annotation
EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014
No description available
Scientific topics: RNA-Seq
Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014
https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Courses/201411-EMBO-High-Throughput-Sequencing-Data-Analysis.md
http://tess.elixir-uk.org/materials/embo-high-throughput-sequencing-data-analysis-cambridge-uk-2014
No description available
RNA-Seq
FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming