The Pluto ATAC-seq workflow
ATAC-seq is a technique used to determine chromatin accessibility on a genome wide scale.
- Start by choosing with project to associate your experiment with, the model organism for your experiment and the experiment type.
- Then, upload your assay data. This can be a FASTQ raw data file or a processed .csv
- Finally, you'll upload sample data for each of the samples in your dataset in a .csv file. Here is an example format for sample data from an ATAC-seq experiment.
- Next, you'll be directed to your experiment overview page where you can add notes to share with collaborators, see how many analyses you've run for that experiment and view uploaded sample data, assay data and the results from the ATAC-seq pipeline.
- You can proceed to the Analysis tab by clicking "Analysis" at the top of the Overview page to start making plots. Press the "+Analysis" button to see what plots are available for your experiment.
The following plot types may be of interest for your ATAC-seq experiment
- Differential Binding Analysis (Heatmap or Volcano plots)
- Principal Components Analysis