How to extract differential peaks from ATAC-seq data? (Using the DiffBind package)

Extracting differential peaks from ATAC-seq data using the DiffBind package involves the following steps:

1. Prepare input data:

First, you need to prepare ATAC-seq data, usually in the form of peak files generated by peak-calling software such as MACS2. For multiple samples, you need to prepare a peak file for each sample.

2. Create a sample sheet:

In DiffBind, you need to create a sample sheet (usually in CSV or Excel format) that contains sample information such as sample names, corresponding peak file paths, and conditions (e.g., treatment and control groups).

3. Read the data:

Use the dba() function of DiffBind to read the sample sheet. This step will integrate the peak data from different samples into a DBA object.

“dbaObj <- dba(sampleSheet = "path/to/your/sampleSheet.csv")”

4. Align and merge peaks:

Use the dba.count() function to align and merge peaks. This step counts the coverage of each peak in each sample.

“dbaObj <- dba.count(dbaObj)”

5. Perform differential analysis:

Use the dba.analyze() function to perform differential analysis. This step identifies peaks that significantly change under different conditions.

“dbaObj <- dba.analyze(dbaObj)”

6. Extract results:

Use the dba.report() function to extract detailed information about the differential peaks. This can be exported as a table, including peak locations and coverage differences under different conditions.

“diffPeaks <- dba.report(dbaObj)”

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