The CosmosID-HUB allows you to store and download your raw fastqs/sequencing data from the dashboard. The video down below gives you a quick walkthrough on how to download the raw fastqs for your samples.

Watch the Tutorial Video Below

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Raw FASTQ files are archived after 14 days following upload

To securely maintain the data, we move large raw data files to our archived storage 14 days after the date of upload. Should you want to download these samples or run additional workflows, you will need to request the data to be removed from the archive.

Unarchiving and raw data maintenance is included with all CosmosID-HUB subscriptions. Non-subscribers wishing to download raw data files may access download links upon request on a per-fee basis.

If your raw data is archived, you will not be able to view the .CSV-formatted Download URLs when selecting "Get Download URLs" from the Export Samples button. To request unarchiving of data, please send the sample list to [email protected].

1. Get Download URLs

Start by selecting your samples in the "Datasets" folder, and select the "Export Samples" → "Get Download URLs"

You can download the URLs in either CSV or TSV format. Open it in a spreadsheet or text app to get the links. The URL column contains the download link for that particular sample (paired-end files will have 2 files with 2 unique URLs).

2a. Paste terminal commands (CURL, POWERSHELL and WGET) to allow easy downloading of raw fastqs from the terminal.

The spreadsheet also contains CURL, POWERSHELL and WGET commands to allow easy downloading of raw fastqs from the terminal. Simple navigate to your desired directory in the terminal and paste each command.

How can you download raw fastqs for multiple samples all at once using UNIX terminal from the download URL CSV/TSV file?

The bash command can be used for downloading multiple files using the download URL CSV/TSV

## Downloading multiple files using download URL CSV
cat samples_download_urls_2023_03_23_21_58.tsv | cut -f4 -d "," | tail -n +1 | while read line; do bash; done

## Downloading multiple files using download URL TSV
cat samples_download_urls_2023_03_23_21_58.tsv | cut -f4 | tail -n +1 | while read line; do bash; done

2b. Paste URL into browser

The "URL" column contains a navigable URL that can be pasted into a web-browser, which will initiate a file download in your browser to the default Downloads folder.

Tutorial: Downloading Raw FASTQ Files