Initiate a Bulk Download

1. Select the samples that you want included in your download by clicking on the checkbox to the left of each sample name. You can select all samples in a project by clicking the checkbox in the table header.
2. Click on the Download button in the upper-right hand corner of the table.
   
   
3. A modal will appear with options for download types. There are two types of downloads: Reports and Raw Data. Reports include metrics computed from the pipeline for the selected samples. Raw Data are the raw reads, contigs, or input files (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
   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 (for Z score metric)
   Contig Summary Reports	csv	Contig QC metrics (e.g. read coverage, percent identity) and other summary statistics

   Raw Data

   Name	File Type	Description	Additional Download Parameters
   Reads (Non-host)	fastq or fasta	Reads with host data subtracted	Taxon to include, desired file type
   Contigs (Non-host)	tar of fasta	Contigs with host data subtracted	Taxon to include
   Unmapped Reads	tar of fasta	Reads that didn’t map to any taxa
   Original Input Files (only available to original uploader!)	tar of fasta	Original files submitted to IDseq

4. If your selected download type requires additional download parameters, make sure to fill our 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.
5. Click Start Generating Download at the bottom of the modal.
6. The modal will disappear and you will see a notification in the upper-right hand corner of your screen. You will see a link in that notification to check on the status of your download.

IDseq 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. When the process is complete, you will be able to download your file from the Downloads page.