Commit c26a9082 authored by Robert Phillips's avatar Robert Phillips
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Update README.md

parent 42a78e71
......@@ -10,10 +10,15 @@ The diagram below outlines a general workflow for the identifcation of enhancers
```mermaid
graph TD;
A-->B;
A-->C;
B-->D;
C-->D;
A[1. For each brain region separately, merge BAM files with SAMtools] --> B[2. For each brain region separately, call peaks with MACS2];
B --> C[3. For each brain region separately, merge peaks within 1kb using bedtools];
C --> D[4. For each brain region separately, remove any peaks smaller than 146 bp or the legnth of DNA wrapped around a nucleosome];
D --> E[5. Combine all peaks with rbind in R. These peaks are the Regions of Open Chromatin or ROCs];
E --> F[6. Keep only intergenic ROCs or iROCs];
F --> G[7. Quantify transcription within iROCs];
G --> H[8. Identify all genes within 1MB up and downstream from TAPE center];
H --> I[9. Correlate eRNA and mRNA transcriptional abundance];
```
## **Study design**
......
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