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Brian Haas edited this page Jun 15, 2018
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- Trinity protocol paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875132/
- Trinity website and documentation: https://github.com/trinityrnaseq/trinityrnaseq/wiki
- Comparing differential expression methods: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-91
- Transcript vs. gene level expression DE: https://www.ncbi.nlm.nih.gov/pubmed/26925227
- Number of sample replicates needed for DE studies: https://www.ncbi.nlm.nih.gov/pubmed/27022035
- Specialty topic: Robust gene network inference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512113/
- Advanced RNA-Seq Data Analysis Course (EBI, Cambridge UK, 2018): http://52.18.118.183:3000/
For those with mixed samples, please explore methods for selecting or depleting sequences based on target alignments
"Get that linux feeling ... on windows" cygwin: https://www.cygwin.com/