Getting Started Guide

Creating an Account

  • Sign up: Brings you to window to create an account

Home Screen

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  • Icons (located on top right corner)
    • Inbox (3rd from the right): Your system messages
    • Selected Samples (2nd from the right): Your selected samples
    • Jobs (rightmost): Your active jobs and their statuses

Creating a Study

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  • Creating a New Study/Edit Study Page
    • Study Title (required): Name of the experiment
    • Study Alias (required): A different name to put your experiment under
    • DOI (optional): Not required but if your paper has already been published you will be given a DOI, or Digital Object Identifier, that scientists can use to find your paper
    • PubMed ID (optional): Not required but if your paper has been published in PubMed it will be given a designated PubMed ID that scientists can use to help find your paper
    • Study Abstract (required): Abstract for your experiment
    • Study Description (required): Quick description of your study, shorter than the abstract
    • Principal Investigator (required): Whose lab it is
    • Lab Person (optional): Who to contact if you have questions about the experiment
    • Environmental Packages (optional): Describing the environment from which a biological sample originates
      • To find out which type of sample you have read this paper found in Nature.
    • Event-Based Data (optional): If your experiment contained interventions you can include that here
      • single intervention, real: a time series with a single intervention on one or more individuals over time
      • multiple intervention, real: a time series with multiple interventions on one or more individuals over time
      • combo intervention, real: a time series with some subjects having one intervention while other subjects have multiple interventions over time
      • single intervention, pseudo: a time series with a single intervention on groups with no subject being present in multiple time points
      • multiple intervention, pseudo: a time series with multiple interventions on groups with no subject being present in multiple time points
      • combo intervention, pseudo: a time series with some groups having one intervention while other groups have multiple interventions on another group with no subject being present in multiple time points
      • single intervention, real: a time series with a single intervention on groups with some subject being present in multiple time points while others are only present in a single time point
      • multiple intervention, real: a time series with multiple interventions on groups with some subject being present in multiple time points while others are only present in a single time point
      • combo intervention, real: a time series with some groups having single intervention while other groups having multiple interventions on groups with some subject being present in multiple time points while others are only present in a single time point
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  • Study Information Page
    • Share: Shares the study with other users
    • Edit: Brings you to the Edit Study Page if you wanted to update your study
    • Delete: Deletes the study
    • Study tags (optional): Keywords that will help you, and others, find your study in Qiita
      • For example, if you’re studying soil you can add that as a tag
      • Must Save tags To keep them otherwise they disappear
    • Sample Information: A link to your metadata summary
    • Upload Files: A link to a screen to upload your files to

Editing a Study

  • Go to the “Study Information Page”
  • Select “Edit” from “Study Information Page” to bring you to “Edit Study Page”
  • Make the desired edits and select “Update Study”

Creating and Working With Sample information

  • The Qiimp tab located at the top of the page is a useful tool for creating Qiita and EBI compatible metadata spreadsheets.

Example files

You can download an example sample information file from here.

EBI-ENA NULL values vocabulary

For all public studies including those being submitted to EBI, no blanks are allowed in the sample information. We support the following null values: not applicable, not collected, not provided, restricted access.

For the latest definitions and explanation visit the EBI/ENA Missing value reporting.

Warning

Column names in your information files cannot be named as a Postgres reserved word. For example, a column cannot be named CONDITION, but could instead be named DISEASE_CONDITION. For a full list of these reserved words, see this link.

Sample information file

The sample information file will define the biological context of each sample, with categories like sample_type, treatment, etc. The sample_name defined in this file is used to relate each sample in the preparation file with the biological sample.

Required fields for Qiita

Note that Qiita require to have at least two columns, including sample_name, for a sample information file to be added to the system:

Field name Format Description
sample_name free text with restrictions Identifies a sample. It is the primary key and must be unique. Allowed characters are alphabetic [A-Za-z], numeric [0-9], and periods ..

Required fields for EBI submission

In order to submit your data to EBI, certain fields are required in your sample information file. You can download a spread sheet containing these required fields on the Knight Lab website under “MetaData Template”.

Attaching the Sample Information to the Study

Upload Sample Information

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  • Upload Files Page
    • Drag your sample info file into the box to upload your files
    • Your uploaded samples will appear under the “Files” section
    • You can currently upload biom tables, .fastq files, .fastq.gz files, among others.
    • For a full list check the upload page of any study.
      • Note that ‘.zip’ files can not be processed.
      • Note that ‘.fasta’ and ‘.fna’ files require ‘.qual’ files for submission.
      • Note that ‘.txt.’ files must be tab separated and require the extension .txt.
    • Delete selected files: Delete a file with the selected boxes
    • Go to study description: Link to the study description page

Attach Sample Information

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  • Sample Information Page
    • Select sample information file: Attaches the uploaded sample information to the study
    • If uploading a QIIME mapping file, select the data type of the prep information: Selects the data type
    • Create: Creates a new sample information page that includes the attached data

Viewing Sample Information

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  • Sample Information Page
    • Sample Information Tab
      • See different metadata values
      • Sample Info: Downloads the metadata onto your computer
      • Update Sample Information: Upload a new sample information file
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  • Sample Information Page
    • Sample-Prep Summary Tab
      • Add sample column information to table: Allows you to add an additional metadata column to the sample summary for comparison on this page

Update Sample info

  • If your data has not been processed…
    • Upload your new metadata file using the Upload Files Page
    • Delete your old metadata file on the Sample Information Page
    • Update your metadata file on the Sample Information tab on the Sample Information page
  • If your data has been processed…
    • Your past metadata file cannot be deleted but fields can be deleted
      • To remove data, go to the Sample Information tab on the Sample Information page and use the trash icon to delete the unwanted fields
    • You can update the fields that do exist (these fields can be found on the sample information tab on the sample information page)
      • Upload a new sample info file including only the updated field data and the sample_name field
    • You can add new fields
      • Upload a new sample info file including only the field data you want to add and the sample_name field
    • Sample names cannot be deleted
      • Any sample name change will be interpreted as a new sample
    • Note that these changes will not update on your analysis but these changes will not affect your processing data since the metadata isn’t applied until analysis

Creating and Working With Preparation information

Prepare information files

The set of required fields for the sample information and preparation information files varies based on the functionality that you want to use from the system.

As described in Qiita Philosophy, a Qiita study can have many biological samples, each with many preparations for different kinds of multi-omic analysis. Thus, the study will have a single sample information file that will define the biological context of each sample. Each multi-omic data type prepared will have a separate preparation information file that will describe the sequencing technology or analytical chemistry used to generate that data set.

To increase the chance of successful meta-analyses we suggest following the Earth Microbiome Protocols and Standards.

Please note that while sample information and preparation information files are similar to a QIIME metadata file, they are conceptually different. A QIIME metadata file includes information about the biological context, like sample_type, and about the wet lab processing, like BarcodeSequence. Qiita intentionally separates this information into two separate files; it would be conceptually incorrect to include BarcodeSequence (barcode) with the sample information, as this information pertains to the wet lab preparation and should be placed in the preparation information file.

Ensure that your prep information column names are correct.

Example files

You can download an example prep information file from here

Required fields for Qiita

Note that Qiita require to have at least two columns, including sample_name, for a prep information file to be added to the system:

Field name Format Description
sample_name free text with restrictions Identifies a sample. It is the primary key, must be unique and should match the ones in the sample information file. Allowed characters are alphabetic [A-Za-z], numeric [0-9], and periods .. Must match the sample_name in the sample template.

Required fields for EBI submission

In order to submit your data to EBI, certain fields are required in your preparation information file. You can download a spread sheet containing these required fields on the Knight Lab website under “Prep Template”.

For all valid values for instrument_model per platform, view the values in the table below:

Platform Valid instrument_model options
LS454 454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX+, 454 GS FLX Titanium, 454 GS Junior, 454 GS Junior or unspecified
Illumina HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500,, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina MiSeq, Illumina MiniSeq, Illumina NovaSeq 6000, NextSeq 500, NextSeq 550, or unspecified

Required fields for pre-processing target gene data

If you are adding target gene data (e.g. 16S, 18S, ITS), there are additional columns that are required for successfully preprocessing them:

Field name Format Description
primer IUPAC characters The primer sequence (this is usually the forward primer for Illumina processed data, or the barcoded primer for LS454 data; examples).
barcode IUPAC characters The barcode sequence (examples).

In case that your data has been sequenced using multiple sequencing lanes or you have Per sample FASTQ files without barcode and primer information, an additional column is required.

Field name Format Description
run_prefix free text Name of your sequence file without the suffix (for example, seqs.fna becomes seqs, and my-data.fastq becomes my-data).

Attaching Preparation Information to the Study

Upload Prep Information

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  • Upload Files Page
    • Drag your data files into the box to upload your files
    • If you want to delete the file, press the box that appears next to that file then click delete selected files
    • Go to study description: Link to the study description page

Attach Prep Information

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  • Study Description Page
    • Choose Add New Preparation
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  • Add New Preparation Page
    • Select File (required): Select the preparatory information file you uploaded
    • Select Data Type (required): Choose for what kind of data you studied
    • Select Investigation Type (optional): Not required, chooses the investigation you performed
    • Create New Preparation: Creates a new preparation based on the data inputted above

Associate Data with Prep Information

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  • Data Type
    • 16S, or the data type you studied dropdown: Shows the preparations created on this type of data on this study
    • Prep Information Page
      • To add files
        • Select Type (required): Select the file type you uploaded, causing Qiita to associate your files with this preparation
        • Add a name for this file (required): Give the file a name
        • Add Files: Shows up after Select Type has been chosen, adds files to the preparation
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  • Prep Information Page
    • Summary Tab
      • Includes preparation info files of that data type that’s associated with your study
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  • Prep Information Page
    • Processing Tab
      • Processing Network: Contains artifacts that represent your data and commands being run on your data
      • Hide: Hides the processing network

Update prep info

  • Prep Information Page
    • Under the “Summary” tab
      • Select “Update Information” and choose your updated file
      • Barcodes and sample names cannot be updated
        • Must create new preparation to update these