This 2 hour seminar will be an interactive discussion and demonstration of the types of applications and work-flows that can be performed on deep sequencing data generated by the latest instruments from Illumina, Life Technologies (SOLiD and Ion Torrent), Roche/454 and others. Applications include the following:
- Data import – Un-aligned reads (FASTQ, .sff etc.) and aligned reads (SAM/BAM)
- Read mapping to reference sequence(s)
- De novo assembly
- Transcriptome assembly
- Digital gene expression analysis by RNA Sequencing
- Exome sequencing by target enrichment
- Variant detection
- ChIP Seq Analysis
- Small RNA analysis
- Curating reference sequences with annotations of interest
- Working with Annotation Tracks
- BLAST – Find and compare genes, protein products and place contigs
- Workflows- Visually Creating and Editing Analysis Pipelines
