- 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.
- Click on the Download button in the upper-right hand corner of the table.
- 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).
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
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
- 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.
- Click Start Generating Download at the bottom of the modal.
- 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.