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- Differential gene expression analysis
- Splice variant analysis
<break> - non-coding RNA analysis annotation - unique mapping (shrimp/grep), miRNA’s abundance/editing, other: snoRNA, snRNA, lincRNA, piRNA, tRNA, degradome, etc. etc. (not poly-A; not annotated)
- Transcriptome assembly & annotation velvet/oases, TrinityRNAseq; BLAST, GOminer, (ELI?)
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- Genome Assembly
- Genome Annotation
- Evaluating & Visualizing assemblies
- Custom Genome Databases Introduction to GMOD and/or SequenceServerAnnotating noncoding RNAs
Resources
- Tool list, file formats & more
- Scott's list of linux one-liners
- Exercises
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