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Commit 4bba5fec authored by Robert Phillips's avatar Robert Phillips
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Update README.md

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...@@ -16,8 +16,9 @@ A[1. For each brain region separately, merge BAM files with SAMtools] --> B[2. F ...@@ -16,8 +16,9 @@ A[1. For each brain region separately, merge BAM files with SAMtools] --> B[2. F
D --> E[5. Combine all peaks with rbind in R. These peaks are the Regions of Open Chromatin or ROCs]; 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]; E --> F[6. Keep only intergenic ROCs or iROCs];
F --> G[7. Quantify transcription within iROCs]; F --> G[7. Quantify transcription within iROCs];
G --> H[8. Identify all genes within 1MB up and downstream from TAPE center]; G --> H[8. Identify iROCs with bidirectional transcription. These are Transcriptionally Active Putative Enhancers or TAPEs]
H --> I[9. Correlate eRNA and mRNA transcriptional abundance]; H --> I[9. Identify all genes within 1MB up and downstream from TAPE center];
I --> J[10. Correlate eRNA and mRNA levels for predicted enhancer-gene pairs];
style A fill:#98EFFF,stroke:#000,stroke-width:2px; style A fill:#98EFFF,stroke:#000,stroke-width:2px;
style B fill:#98EFFF,stroke:#000,stroke-width:2px; style B fill:#98EFFF,stroke:#000,stroke-width:2px;
style C fill:#98EFFF,stroke:#000,stroke-width:2px; style C fill:#98EFFF,stroke:#000,stroke-width:2px;
...@@ -26,7 +27,8 @@ A[1. For each brain region separately, merge BAM files with SAMtools] --> B[2. F ...@@ -26,7 +27,8 @@ A[1. For each brain region separately, merge BAM files with SAMtools] --> B[2. F
style F fill:#98EFFF,stroke:#000,stroke-width:2px; style F fill:#98EFFF,stroke:#000,stroke-width:2px;
style G fill:#98EFFF,stroke:#000,stroke-width:2px; style G fill:#98EFFF,stroke:#000,stroke-width:2px;
style H fill:#98EFFF,stroke:#000,stroke-width:2px; style H fill:#98EFFF,stroke:#000,stroke-width:2px;
style I fill:#98EFFF,stroke:#000,stroke-width:2px; style I fill:#98EFFF,stroke:#000,stroke-width:2px;
style J fill:#98EFFF,stroke:#000,stroke-width:2px;
``` ```
## **NGS Experimental Details** ## **NGS Experimental Details**
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