Perform Functional Annotation Analysis in Pluto for all your epigenetic sequencing experiments
Want to annotate genes or genomic features after identifying consensus peaks? Pluto's functional annotation analysis type allow you to do that for CHiP-seq, ATAC-seq and CUT&RUN experiments.
What is Functional Analysis?
Functional analysis allows you annotate locations within the genome and identify the relative location relationship between identified peaks and gene or genomic features such as 3ʹUTRs, promoter regions or exons. This enables a variety of insights into the regulation of gene expression including gene targets of transcription factors and histone modifications or functional implications of epigenetic changes for various biological processes or disease states.
Functional Annotation Analysis in Pluto
This analysis type is available for data using our CHiP-seq, ATAC-seq and CUT&RUN experiment types.
Once you have one of these experiments open, you can start your Functional Annotation by navigating to our Analysis button to pull up the types of analyses you can do on your experiment.
From there, scroll down to the "Genome" section where you'll see the options to make a stacked bar plot or pie chart. Choose the type of plot you're interested in making.
For the stacked bar plot, you'll be directed to select the kind of peak you're interested in such as sample, consensus or differentially bound peaks. You can also adjust the transcription start site region and select the genome for your analysis. This analysis takes a few minutes to run, so you can always close the analysis pop up while you're waiting. 
After your analysis finishes running, you'll be able to see the plot you've made and customize the plot title, colors and legend. 
For the pie chart, start a new analysis and navigate to the "Genome" section of the analysis tab to locate the "Pie Chart" for functional annotation analysis
Once you've selected pie chart, you can choose what peaks you'd like to look at. When you select differentially bound peaks, you'll be prompted to choose your comparison of interest for your plot. You can also adjust the transcription start site region and select the genome for your analysis.
Now you can customize your pie chart with a custom plot title, colors and legend.
