Peak Calling Analysis

Your Possible Next Steps

Genome browsers

  • Ultimately, to get a good sense of your data and to browse your favorite genes, you will need to load your data into a genome browser. Two commonly used genome browsers are the UCSC web browser and the IGV software.
  • The UCSC web browser is your browser of choice if you would like to look at your ATAC-seq peaks alongside already published annotation that is pre-loaded in the browser. To use the UCSC web browser, open the genome browser, choose the genome of interest, and upload your data via “My Data” → “Custom Tracks”. It may be that the UCSC web browser complains about your peak files. In that case, separately save only the essential information (chromosome, start, end) in a bed file, and try again.
  • IGV is your browser of choice if you would like to look at your data in more detail and load various kinds of data formats. In any case, it is a good idea to get IGV installed. If you cannot install IGV yourself, please write a trouble ticket to the IT team. To use the IGV browser, open the IGV session produced by Nfcore.
    • Location: igv/<PEAK_TYPE>/igv_session.xml
    • This will automatically load the genome, the coverage tracks (bigwig) and called peaks (broadPeak, narrowPeak). If you are interested in seeing the individual reads, open the respective bam files as well. If you’d like to load published data alongside, you can do that easily by loading more tracks.
    • To be able to look at genes, you need to load your favorite annotation. For example, this is a mouse Ensembl gene annotation.

Functional enrichment analysis

  • If you want to learn about the function of genes that are associated to your ATAC-seq peaks, you can run a functional enrichment analysis with GREAT. Again, you might need to adapt your peak files and save the essential information (chromosome, start, end) in a bed file.