Import data from Genewiz, Novogene, and other sequencing providers directly into Pluto for processing
Overview
Inputting FTP credentials when creating your experiment in Pluto
1. Create a new experiment in Pluto and select the appropriate type of sequencing assay, such as ChIP-seq. Click Continue.
2. On the Assay Data page, go to the Other tab and click the grant Pluto access or provide credentials link under the "Import from other storage locations (FTP)" section.
3. Enter the FTP credentials provided by your sequencing vendor. If you have any trouble finding the required fields, feel free to reach out to our team at support@pluto.bio or using the chat bubble in the lower right corner of the screen. After clicking Submit, it is safe to close the form.
4. Back in the experiment wizard, it's safe to click the Skip button to continue past the assay data and sample data steps of the wizard. You will see the purple banner indicating the experiment has been created and is in a draft state.
5. Your import will begin and may take a few minutes to a few hours depending on the number and size of FASTQ files to be imported. If you return to the experiment while files are being imported, you'll see a light blue banner on the experiment overview page.
6. You'll receive an email notification when the import has completed! Click the Go to experiment button to edit the sample annotations and kick off a pipeline with your raw data.
7. On the assay data step (step 2 of 4 in the wizard), you'll see that FASTQ files have now been uploaded to the experiment. No action is needed from you here, click Continue to go to the next step.
8. On the sample annotation step (step 3 of 4 in the wizard), a draft sample annotation table has been started for you. Download this table using the download icon to the right of the file name.
9. Open the file in Excel or another spreadsheet editor. You'll see that the table contains a set of sample IDs matched to the FASTQ files that were imported via FTP. It also contains a placeholder condition column - this is where you'll edit the spreadsheet here to represent your experimental design.
10. Edit the ? vales in the existing placeholder column, or replace the placeholder with any number of additional columns representing your experimental design. For example, the completed version of the spreadsheet above may look like this:
In the above spreadsheet, we've added columns for treatment, cell_line, and replicate. You should add columns that represent each of the variables in your experiment set-up, such as genotype, dose, timepoint, etc. Column names cannot contain spaces or special characters except hyphens.
11. Back in the Pluto experiment wizard, click the red X icon to remove the draft sample data table. Then, upload your completed table. A pop-up window will let you view your uploaded table and make any final edits. Click Confirm once finished.
12. On the fourth and final step of the experiment wizard, you'll be asked to select parameters for the pipeline, which will convert the FASTQ files from your sequencing vendor into a count matrix for downstream analysis. The pipeline parameters will vary based on the kind of assay your data came from.
Questions or need help? Feel free to chat with us or email support@pluto.bio for assistance!