The Eel Pond mRNAseq Protocol¶
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This is a lightweight protocol for assembling up to a few hundred million mRNAseq reads, annotating the resulting assembly, and doing differential expression with RSEM. It is part of khmer-protocols; see the main page for this version for citation information, and the khmer-protocols site for the latest released version.
Special thanks to Dr. Joshua Rosenthal for his help in developing this, and to Dr. Leslie Babonis for her feedback on various problems!
The tutorial:
- 0. Downloading and Saving Your Initial Data
- 1. Quality Trimming and Filtering Your Sequences
- 2. Applying Digital Normalization
- 3. Running the Actual Assembly
- 4. BLASTing your assembled data
- 5. Building transcript families
- 6. Annotating transcript families
- 7. Expression analysis (with RSEM)
- 8. Differential expression (with EBSeq)
Reference material¶
LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github.
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