Explore our CUT&RUN analysis road map in Pluto
Streamlined analysis for your CUT&RUN experiment to identify DNA-protein interaction sites.
1. Create Experiment
2. Upload sample and assay data
First, you'll add your assay data as a FASTQ or .csv file. For a FASTQ, your file when then undergo a series of preprocessing steps including the trimming of adapter sequences, alignment to the reference genome chosen when creating the experiment, filtering, peak calling and binding site identification.
If you have a processed .csv file, you can upload that count matrix with consensus peaks using the "csv" tab.
3. Then you will add your sample annotations with a .csv file containing the sample IDs from your assay data. Here is an example
4. From here your data will be run through the pipeline and these downstream analyses will be available to you.
- Differential Binding (Heatmap and Volcano plots)
- IGV Peak plot
- Coverage (Tornado and Profile plots)
- Transcription Factor Enrichment analysis (Score Bar Plot)
- Gene Set Enrichment
- Summary Analysis (CPM normalized or raw values)
If you upload a .csv file for your assay data, you will not be able to generate Tornado, profile and IGV plots.