This RNA-seq workshop will address critical issues related to Transcriptomics data, like:
Processing raw Next Generation Sequencing (NGS) data:
1. Next Generation Sequencing data preprocessing: Trimming technical sequences Removing PCR duplicates
2. RNA-seq based quantification of expression levels: Conventional pipelines (looking at known transcripts) Identification of novel isoforms Analysis of Expression Data Using Machine Learning:
3. Unsupervised analysis of expression data: Principal Component Analysis Clustering
4. Supervised analysis: Differential expression analysis Classification, gene signature construction
5. Gene set enrichment analysis
The workshop will include hands-on exercises utilizing public domain datasets: breast cancer cell lines transcriptomic profiles (https://genomebiology.biomedcentral.c…), patient-derived xenograft (PDX) mouse model of tumor and stroma transcriptomic profiles (http://www.oncotarget.com/index.php?j..), and processed data from The Cancer Genome Atlas samples (https://cancergenome.nih.gov/).
Team: The workshops are designed by the researchers at the Tauber Bioinformatics Research Center at University of Haifa, Israel in collaboration with academic centers across the US. Technical support for the workshops is provided by the Pine Biotech team.