Initiate a Bulk Download

Overview

You can download data and/or reports for multiple samples from any Project page. After initiating a bulk download, files will be created in the Downloads page. Please note that files available through the Downloads page will be deleted after 7 days of creating the download.

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Downloading Samples 

To download data from the Project page, select the sample(s) for download and click the Download icon () on the right-hand side of the page. You can select all samples in a project by clicking the checkbox in the table header.

A modal will appear with options for download types, including Reports and Raw Data. Select the download file and click “Start Generating Download”. CZ ID will now start preparing your data for download. This involves calculating and compiling the data from the various samples you selected into a single file that is ready to download. This process can take several hours if hundreds of samples are selected.  

Below is a list of available download files. Reports include metrics computed from the pipeline for the selected samples. Raw Data includes raw reads, non-host reads, and contig sequence files. Note that raw data files are only accessible for the original uploader.

Reports

Name	File Type	Description	Additional Download Parameters
Sample Overviews	CSV	Sample QC metrics (e.g. percent reads passing QC) and other summary statistics	N/A
Sample Taxon Reports	CSV	Computed metrics (e.g. total reads, rPM) and metadata for each taxon identified in the sample	Background Model (to calculate Z score)
Combined Sample Taxon Results	CSV	The value of a particular metric (e.g. total reads, rPM) for all taxa in all selected samples, combined into a single file	Metric, Background Model (if Z score metric is selected)
Contig Summary Reports	CSV	Contig QC metrics (e.g. read coverage, percent identity) and other summary statistics	N/A
Combined Microbiome File	BIOM	The value of a particular metric (e.g. total reads, rPM) for all taxa in the selected samples combined with all sample and taxon metadata. This file can be uploaded to MicrobiomeDB for the calculation of microbiome stats (e.g. alpha diversity, relative abundance)	Metric, Threshold filters (optional), Background Model (if Z score metric is selected)

 

Raw Data

Name	File Type	Description	Optional Download Parameters
Reads (Non-host)	FASTQ or FASTA	Reads with host data subtracted	Taxon to include, desired file type
Contigs (Non-host)	FASTA (Compressed as ".tar" file)	Contigs with host data subtracted	Taxon to include
Unmapped Reads	FASTA (Compressed as ".tar" file)	Reads that didn’t map to any taxa	N/A
Original Input Files (only available to original uploader)	FASTQ (Compressed as ".tar" file)	Original files submitted to CZ ID	N/A

Note: If your selected download type requires additional download parameters, make sure to fill out that information in the modal after you select the download type. Hint! To search for a taxon, start typing in the search box to see a list of matching results to choose from.

The modal will disappear after selecting a file and initiating the download. You will see a confirmation in the upper-right hand corner of your screen. Go to the Downloads page to check on the download status and download generated files. Download files will be available for 7 days after creating the download.