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- [MOFA](https://github.com/PMBio/MOFA) was used to analyze RNA-seq data
- and ChIP-seq data for 3 histone marks together, looking for sources of
- variation shared acorss all data types. Two different analyses were
- done, one with ChIP-seq reads counted in promoter regions, and one
- with ChIP-seq reads counted in called peaks. Each analysis is split
- into two steps. The first step ("run") is fitting the model (which
- takes a long time) and performing some basic QC, while the second step
- ("analyze") loads the fitted model and performs some analysis.
- ## Peak-based analysis
- - Step 1: [`peak-mofa-run.html`](peak-mofa-run.html)
- - Step 2: [`peak-mofa-analyze.html`](peak-mofa-analyze.html)
- ## Promoter-based analysis
- - Step 1: [`promoter-mofa-run.html`](promoter-mofa-run.html)
- - Step 2: [`promoter-mofa-analyze.html`](promoter-mofa-analyze.html)
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