Experiment types in Pluto
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      ChIP-seq - FASTQ upload

      Run the ChIP-seq pipeline on Pluto with a raw data upload

      Identify transcription factor binding sites to see how your DNA binding proteins are regulating gene expression  with our ChIP-seq pipeline.

      Step 1. Create your experiment.

      Start by choosing with project to associate your experiment with, the model organism for your experiment and the experiment type. 

      Step 2. Upload your assay data.

      Here you'll upload a FASTQ or other raw data file for processing through our pipeline. Once the data has uploaded, you'll see your raw data files populated below in the "uploaded files" section.

      Step 3. Upload your sample annotations.

      Next you'll upload sample data in a .csv format with annotations for each of the samples in your dataset. Within this window, you can download a template to generate your sample annotations as a .csv or google sheet.


      Here is an example of a sample annotation file for a ChIP-seq experiment.

      Step 4. Configure your pipeline settings

      With a raw data upload, you'll be able to configure some parameters for the pipeline that will be run on your raw sequencing files.  Here you'll enter information about the genome annotation you'd like to use, the library type and peak caller.

      Genome - This field will populate with available genome annotations based on the organism you chose when creating the experiment. If this dataset is part of a larger experiment, make sure to select the same genome as your previous analyses in Pluto.

      Library type - Paired end or single end. This is dependent on how your libraries were prepared for sequencing. 

      Peak Caller - On Pluto, you have the choice between MACS2 and SEACR for peak calling. Check out this article if you'd like some extra guidance on how to choose your peak caller. You'll also see some extra settings for peak type (narrow or broad) and peak p-value cutoff.

      From here you'll be taken to your Experiment Overview page where you can add an experiment overview such as comments on your experiment, track plots created and view sample data, assay data, results from your analyses and any attachments you've added to your experiment.

      Step 5. Start your analyses!

      From here, you can head to the analysis tab and use the +Analysis button to start creating plots.

      For ChIP-seq we have these plot types you may be interested in making for your data. With raw data files, you'll have access to all possible plot types with the experiment.