The avatar for @josesho
Joses W. Ho
Estimation statistics, craft beer, data visualization, web scraping, poetry
Public
Edited
May 29, 2023
1 star
Insert cell
Insert cell
Insert cell
htl.html`<pre>${samtoolsOut.stdout}</pre>`
Insert cell
samtoolsOut = cliObj.cli.exec(
"samtools view /shared/data/test.bam 20:39,352,829-39,352,842"
)
Insert cell
await cliObj.cli.mount([
{ name: "test.bam", url: bamURL },
{ name: "test.bam.bai", url: baiURL }
])
Insert cell
bamURL = "https://1000genomes.s3.amazonaws.com/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
Insert cell
baiURL = bamURL + ".bai"
Insert cell
Insert cell
htl.html`<pre>${minimapOut.stdout}</pre>`
Insert cell
minimapOut = cliObj.cli.exec(
"minimap2 -a /minimap2/MT-human.fa /minimap2/MT-orang.fa"
)
Insert cell
Insert cell
cliObj = ({
cli: await new Aioli(["samtools/1.10", "minimap2/2.22"], {
printInterleaved: false
})
})
Insert cell
Aioli = require("@biowasm/aioli@3.1.0/dist/aioli.js")
Insert cell

One platform to build and deploy the best data apps

Experiment and prototype by building visualizations in live JavaScript notebooks. Collaborate with your team and decide which concepts to build out.
Use Observable Framework to build data apps locally. Use data loaders to build in any language or library, including Python, SQL, and R.
Seamlessly deploy to Observable. Test before you ship, use automatic deploy-on-commit, and ensure your projects are always up-to-date.
Learn more