Frequently Asked Questions¶
Qiita data disclaimer¶
Qiita is a research tool, and as such, is hosted on research computing resources maintained by the Knight Lab at the University of California San Diego.
Data privacy is a key aspect of our operations, and is strictly adhered to at every step of the workflow. We are committed to protecting any and all information (including sequence data) submitted to Qiita. For example, your data is sandboxed by default upon upload, and remains private at the discretion of the Owner (i.e., you are the Owner) of the study.
Authorizations and access associated with any given study is maintained and controlled by the Owner of the study; importantly, this means that sharing rights of a study within Qiita is determined solely by the Owner.
A study within Qiita, and its associated sequence and metadata, can be permanently deleted by the Owner as long as it is not public.
What kind of data can I upload to Qiita for processing?¶
Processing in Qiita requires 3 things: raw data, sample and prep information files. Here you can find a list of currently supported raw files files. Note that we are accepting any kind of target gene (16S, 18S, ITS, whatever). You can also upload WGS however, WGS processing is not ready.
What’s the difference between a sample and a prep information file?¶
A sample information file describes the samples in a study, including environmental factors relating to the associated host. The prep information file has information on how the sample was processed in the wet lab. If you collected 100 samples for your study, you will need 100 rows in your sample information file describing each of them, and additional rows for blanks and other control samples. If you prepared 95 of them for 16S and 50 of them for 18S, you will need 2 prep information files: one with 95 rows describing the preparation for 16S, and another one with 50 describing the 18S. For a more complex example go here and for examples of these files you can go to the “Upload instructions” here.
Example study processing workflow¶
A few more instructions: for the example above the workflow should be:
Create a new study.
Add a sample information file. You can add 1, try to process it and the system will let you know if you have errors or missing columns. The most common errors are: the sample name column should be named sample_name, duplicated sample names are not permitted. For a full list of required fields, visit Getting Started Guide.
Add a prep information file to your study for each data type. The prep information file should contain all the samples in the sample information file or a subset. If you have more than one FASTQ file set (forward, reverse (optional) and barcodes) you will need to add a run_prefix column, see Prepare information files. A prep information file and a QIIME compatible mapping file will be available for download after the prep information file is added successfully.
Upload and link your raw data to each of your prep information files. Depending on your barcoding/sequencing strategy you might need 1 or more raw data file sets. If you have 2 raw data sets you may have to rename one set so that each set has a different name. If they have the same name they will over-write on upload. Note that you can have one FASTQ file set linked to more than one prep information file.
Preprocess your files. For target gene amplicon sequencing, this will demux and QC. There are multiple options for preprocessing depending on the barcode format and the data output from the sequencing center - this may require a series of trial and error to establish the correct option for your data files. After demultiplexing a log file is generated with statistics about the files demultiplexed including the number of sequences assigned per sample.
Process each of your preprocessed data types. For target gene, this will perform closed OTU picking against the latest version of Greengenes and can be quite time consuming depending on the number of samples and the depth of sequencing.
How to solve download or unzip errors?¶
Dealing with large files might be daunting but, in general, following these instructions should make things easier. First, make sure that you have enough space for the zip download file; if you are unsure of the size required click on the button and your browser will show an estimate size of the download. Second, make sure that your computer has all the sleep settings turned off; for example, in a Mac, got to System Preferences, Energy Saver, Power Adapter and unselect the option of “Put hard disks to sleep when possible”; don’t forget to save the settings. Third, download the file but point to the storage that you want to save your file in; using Chrome, right click on the download button and select “Save Link As …”; and select the location where you have enough space (see point 1). Fourth, wait for the download to finish, this will depend on your Internet service. Finally, unzip the file with a newer version of zip (see below).
By the way, if you are a developer and would like to add to Qiita the possibility of resumable downloads, we would happily welcome this contribution.
Now, when trying to open the large downloaded zip file there is a change that you will get an error like: “start of central directory not found; zipfile corrupt”. This issue arises from using old versions of zip and you need to have unzip >= 6.0.0. To check you unzip version you can run: unzip -v.
To update your unzip for most operating systems you can simply use your regular package admin program. However, for Mac we suggest using this version of unzip.
Do you have general analytical questions?¶
Normally these are: How can I test X factor in my samples? Why do I see this pattern? Which statistical method better fits my question?
As you can imagine, you are not alone as this is a common problem while doing analysis. Thus, we suggest posting your question to the QIIME2 Forum. This will generally ensure that your question is answered in a timely manner. There are many users and developers monitoring the QIIME2 Forum. Posting questions in the forum allows you to share answers with others, who may have similar questions in the future.
Do you have Meta-Analysis questions?¶
A common thing is why do I have a given pattern in my analysis, like PCoA plots or taxonomy summaries.
Let’s start by saying, this is an open area of research so we are still learning about the effect sizes and what matters in individual and meta-analysis. However, there are a few good resources to help you understand those patterns:
How to solve BIOM name errors?¶
When uploading a BIOM table, you may get an error like: “The sample ids in the BIOM table do not match the ones in the prep information. Please, provide the column “run_prefix” in the prep information to map the existing sample ids to the prep information sample ids.”. This issue arises if your sample names in your BIOM table do not match with the sample names in your preparation information file.
To correct this issue, simply add a column to your preparation information file named “run_prefix”. In this column, add the sample names from your BIOM table that matches the sample names listed in the sample_name column in your preparation information file.
How to convert Qiita files to QIIME2 artifacts?¶
How to cite Qiita?¶
If you use Qiita for processing, submition to EBI-ENA and/or its data for any published research, please include the following citation:
Qiita: rapid, web-enabled microbiome meta-analysis. Antonio Gonzalez, Jose A. Navas-Molina, Tomasz Kosciolek, Daniel McDonald, Yoshiki Vázquez-Baeza, Gail Ackermann, Jeff DeReus, Stefan Janssen, Austin D. Swafford, Stephanie B. Orchanian, Jon G. Sanders, Joshua Shorenstein, Hannes Holste, Semar Petrus, Adam Robbins-Pianka, Colin J. Brislawn, Mingxun Wang, Jai Ram Rideout, Evan Bolyen, Matthew Dillon, J. Gregory Caporaso, Pieter C. Dorrestein & Rob Knight. Nature Methods, volume 15, pages 796–798 (2018); https://doi.org/10.1038/s41592-018-0141-9.