2. Materials and Methods
2.2. Procedures for enChIP-Seq
2.3. Filtering of the NGS Peaks to Identify Genomic Regions Interacting with a Target Locus
2.4. Preparation of the Data Set
2.5. Mode of Analysis
2.6. Handling of the System
2.6.1. Extraction of Peak Information Commonly Included in Two or More Tab Files
2.6.2. Elimination of Negative Peak Information
2.6.3. Data Export
2.6.4. View Information within a Tab File
- The information within a tab file can be viewed directly in the software program. To this end, add one tab file that includes enChIP-specific NGS peaks in the field “I” (or “II”).
- Click on “view” in the field “I” (or “II”) to view the information within the file.
- The information is shown in “V”.
3. Results and Discussion
- Step 1:
- We compared the data from “enChIP #6 peaks” and “Off-target sites” to eliminate off-target binding sites. The resultant information was named “enChIP #6-specific sites”.
- We compared the data from “enChIP #17 peaks” and “Off-target sites” to eliminate off-target binding sites. The resultant information was named “enChIP #17-specific sites”.
- To identify peaks with confidence, we adopted two criteria for choosing peaks based on NGS information from the target 5′HS5 locus: (i) Tag number ≥5% of that of the target 5′HS5 locus (which can be considered as an interacting ratio of ≥5%) and (ii) fold enrichment relative to input genomic DNA ≥10. In this regard, 19 and 228 peaks for “enChIP #6-specific sites” and “enChIP #17-specific sites”, respectively, passed the two criteria.
- Step 2:
- We compared the data from “enChIP #6-specific sites” and “enChIP #17-specific sites” to extract “enChIP #6/#17-common sites”. We extracted six peaks, which can be considered bona fide physically interacting genomic regions (Figure 5B). These results were consistent with those from our previous study  (please note that in Ref. , the symbols > should have been ≥).
5. Availability and Requirements
- Project name: enChIP-Seq analyzer
- Software homepage (GitHub): https://github.com/TKY-SE/enChIP-Seq-Analyzer, accessed on 1 December 2021
- Programming language: Java
- Other requirements: Windows machine
- License: None
- Any restrictions to use by non-academics: None.
- Notes: We have a plan to adapt the software for Linux and Mac. As soon as they are available, we will upload the code in GitHub
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
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