Raw FASTQ files are only accessible for 14 days after upload, after which the files are moved to archives for 1 year. When archived, the data is unavailable for direct download or workflow use. To unarchive, please email your sample list to support@cosmosid.com; a $500 fee applies.

1

Get Download URLs

Start by selecting your samples in the “Cohorts and Metadata” menu, and select the “Export Samples” → “Get Download URLs” to generate download links in either CSV or TSV format.

2

Open the file in a spreadsheet or text app (i.e., Excel)

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).

Downloadlinks Pn

3

Use the generated URLs or preformatted commands (CURL, POWERSHELL, or WGET) to download raw fastqs

Browser Method:
Paste URLs from the “URL” column directly into your web browser to initiate the download to your default Downloads folder.

Terminal Method:
Use the provided preformatted commands (CURL, POWERSHELL, or WGET) from the spreadsheet. Simply navigate to your target directory in the terminal and paste the commands.

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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
tail -n +2 samples_download_urls_2023_03_23_21_58.csv | cut -d',' -f6 | while read url; do
    wget "$url"
done

## Downloading multiple files using download URL TSV
tail -n +2 samples_download_urls_2023_03_23_21_58.tsv | cut -f6 | while read url; do
    wget "$url"
done