While the genome in an organism is considered to be mostly static over time, changes associated with development, aging and disease is reflected in the transcriptome. Comparative studies applying RNA-seq enables investigation of changes in expression level, isoform usage and regulatory events as circularization.
While each project is unique and consequently the optimal solution varies accoring to the settings, some elements are will the be fairly consistent across most experiements.
Additional Bioinformatic Analysis for Total RNA sequencing
Pathway analysis (Gene ontology analysis, Pathway enrichment analysis
Network analysis, including Condition specific expressed analysis, Gene Co-expression Network
Analysis, Time series analysis
CircRNA detection and circRNA differential expression analysis
Alternative splicing/isoform usage analysis/Fusion gene analysis
LncRNA detection and function prediction /LncRNA Family prediction and classification
SNP and Indel detection
Protein-Protein Interaction (PPI) analysis
Comparison with online available data (Data-mining)