To open a folder or a file preview in a new window, hold down the Cmd or Ctrl key while clicking the file/folder name.
To browse an s3://
or gs://
path, simply append it to 42basepairs.com/
!
For example, to browse s3://giab/data/NA12878
, go to
42basepairs.com/s3://giab/data/NA12878
If you use a path that corresponds to a file, you will be redirected to its parent folder, where the file will be highlighted.
First, get the download URL by clicking the file's Copy download URL button. Then:
curl -O "https://42basepairs.com/download/r2/genomics-data/alignments_NA12878.bam"
You can replace wget
in the command above if you don't have have curl
on your machine.
The download URL can be programmatically infered without using the UI:
42basepairs.com/download/cloudProvider/bucketName/path/to/file
where cloudProvider is either s3
, gs
, or r2
.
Some bioinformatics tools such as samtools
and bcftools
support URLs, so you don't need to download the entire file locally
before running a query.
To subset a small region from a large .bam
:
samtools view "https://42basepairs.com/download/r2/genomics-data/alignments_NA12878.bam" 11:93646751-93647750
To subset a small region from a large .vcf
:
bcftools view "https://42basepairs.com/download/r2/genomics-data/variants_CHM13.vcf.gz" chr18:50e6-60e6
These commands will automatically download the much smaller .bai
or .tbi
index files from 42basepairs into the current folder,
so they can be used to download only a subset of the data.
You can use 42basepairs download URLs in your web applications to fetch public genomics data from the front end, as the URLs are CORS-enabled.
Refer to the biowasm docs if you're interested in lazy-loading those download URLs, and running small analyses in the browser.