Overview of Small exRNA-seq Data Submission to the DCC (via FTP Pipeline)

This Wiki page includes instructions on how to submit your small exRNA-seq data (with accompanying metadata) to the Data Coordination Center (DCC)
using the Genboree FTP Data Submission Pipeline.

Things to Know Before Submission

This tutorial will walk you through the entire process of creating an FTP account, formatting and submitting your data and metadata properly,
and then collecting the results. All submitted samples will be processed through the exceRpt Small RNA-seq Pipeline for exRNA Profiling
and exceRpt Small RNA-seq Post-processing tools.

Step 0: Getting an FTP Account on the Genboree FTP Server

Creating Your FTP Account

Small exRNA-seq Data Submission Pipeline

Files Needed for Data Submission

Your submission will consist of three different files:
  • a data archive: The data archive will contain all of your different data files (FASTQ / SRA) as well as an optional spike-in file (FASTA) for those inputs.
  • a metadata archive: The metadata archive will contain various metadata documents relating to your data submission.
  • a manifest file: The manifest file will link together your data and metadata files, and it will also provide other valuable information for verifying that your submission is complete.

IMPORTANT NOTE
All three files must have the same file name, other than the data archive file name ending in _data and the metadata archive file name ending in _metadata.
This will be explained again in Step 4 below, but your files will look something like this:

  • samples_data.zip
  • samples_metadata.zip
  • samples.manifest.json

Here, I've chosen the name "samples" for my submission. This is just an example - you should give a more descriptive name in your actual submission ("gastricCancerOct2015_data.zip", for example).

Step 1: Preparing Your Data Archive

Prepare Your Data Archive

Step 2: Preparing Your Metadata Archive

Prepare Your Metadata Archive

Step 3: Preparing Your Manifest File

Prepare Your Manifest File

Step 4: Uploading Your Submission to the FTP Server for Processing

Upload Submission to the DCC using FTP Server


Step 5: Viewing Your Results

Viewing Your Results


IMPORTANT NOTE
Please read the e-mail carefully. It is possible that some of your submitted files were not
processed correctly (due to some issue with the FASTQ / SRA file, most likely). If this is the case,
please read the What If My Submission Fails? section below for some advice on fixing those failed files.

What If My Submission Fails?

Troubleshooting

Miscellaneous Tips and Tricks

Below, you'll find some useful tips and tricks for creating your submission for the FTP Pipeline.

Creating an Archive

Creating an Archive

Learning How to Use the Terminal

If you need help navigating the terminal (and want to learn some basic Linux/OSX commands), the following links will be useful:

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