Overview of Data & Metadata Submission to the DCC (via FTP Pipeline)

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

If you're submitting small RNA-seq data, you should follow the steps in the "Small RNA-seq Data Submission Pipeline" section.
If you're submitting long RNA-seq data, you should follow the steps in the "Long RNA-seq Data Submission Pipeline" section.
If you're submitting qPCR data, you should follow the steps in the "qPCR Data Submission" section.

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 seeing your dataset on the Atlas.

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

Creating Your FTP Account

Small RNA-seq Data Submission Pipeline

All submitted samples will be processed through the exceRpt Small RNA-seq Pipeline for exRNA Profiling
and exceRpt Small RNA-seq Post-processing tools.

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, the metadata archive file name ending in _metadata, and the manifest file name ending in .manifest.json.
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: Processing Your Files

Processing Your Files

Long RNA-seq Data Submission Pipeline

Files Needed for longRNAseq Data Submission

Your submission will consist of three different files:
  • a data archive: The data archive will contain all of your different paired-end reads FASTQ data files.
  • 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 _longRNAseq_data, the metadata archive file name ending in _longRNAseq_metadata, and the manifest file name ending in .manifest.json.
This will be explained again in Step 4 below, but your files will look something like this:

  • samples_longRNAseq_data.zip
  • samples_longRNAseq_metadata.zip
  • samples_longRNAseq.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_longRNAseq_data.zip", for example).

Step 1: Preparing Your longRNAseq Data Archive

Prepare Your longRNAseq Data Archive

Step 2: Preparing Your longRNAseq Metadata Archive

Prepare Your longRNAseq Metadata Archive

Step 3: Preparing Your longRNAseq Manifest File

Prepare Your longRNAseq Manifest File

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

Upload longRNAseq Submission to the DCC using FTP Server

Step 5: Processing Your longRNAseq Files

Processing Your longRNAseq Files

qPCR Data Submission

Files Needed for qPCR Data Submission

Your submission will consist of two or three different files:
  • a data archive: The data archive is OPTIONAL. It will contain all of your different data files (RDML format or any other custom format provided by the qPCR instrument).
  • a metadata archive: The metadata archive will contain various metadata documents relating to your data submission.
  • a manifest file: The manifest file will provide valuable information about your submission.

IMPORTANT NOTE
Both files must have the same file name, other than the data archive file name ending in _qPCR_data, the metadata archive file name ending in _qPCR_metadata, and the manifest file name ending in .manifest.json.
This will be explained again in Step 3 below, but your files will look something like this:

  • samples_qPCR_data.zip
  • samples_qPCR_metadata.zip
  • samples_qPCR.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_qPCR_data.zip", for example).

Step 1: Preparing Your qPCR Data Archive

Prepare Your qPCR Data Archive

Step 2: Preparing Your qPCR Metadata Archive

Prepare Your qPCR Metadata Archive

Step 3: Preparing Your qPCR Manifest File

Prepare Your qPCR Manifest File

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

Upload qPCR Submission to the DCC using FTP Server

Step 5: Processing qPCR Your Files

Processing Your qPCR Files

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 link will be useful:

Also available in: HTML TXT