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chore(portal): update FAQ: replace GEMINI with VCF and add igv.js men…
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davidlougheed committed Jan 4, 2024
1 parent cd978c7 commit 61be70c
Showing 1 changed file with 9 additions and 10 deletions.
19 changes: 9 additions & 10 deletions client/src/components/pages/FAQPage.js
Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,10 @@ const FAQPage = () => {
<p>
To generate plots, we either use pre-computed, batch-corrected and normalized sample-wise signal matrices,
or use the UCSC <em>bigWigSummary</em> tool to calculate average signal across a feature for each sample
upon request. These values are combined with genotype information extracted from a{" "}
<a href="https://gemini.readthedocs.io/en/latest/"
target="_blank"
rel="noreferrer">Gemini database</a> into a box plot on a server, which is
then sent to the user’s browser if they have signed in and agreed to the terms of use. Plots are generated
as needed, rather than in advance, and are derived directly from the matrix or track and genotype data.
upon request. These values are combined with genotype information, extracted from a VCF file, to create a
box plot on a server, which is then sent to the user’s browser if they have agreed to the terms of use.
Plots are generated as needed, rather than in advance, and are derived directly from the matrix or track and
genotype data.
</p>
</details>
<details open={true}>
Expand All @@ -24,10 +22,11 @@ const FAQPage = () => {
We generate{" "}
<a href="https://genome.ucsc.edu/"
target="_blank"
rel="noreferrer">UCSC Genome Browser</a> track hubs upon
request to visualize averaged normalized track segments for a given genomic feature. These averaged tracks
are created on the fly by averaging bigWig regions of samples sharing an experimental treatment and
genotype, using our command-line tool:{" "}
rel="noreferrer">UCSC Genome Browser</a> track hubs or{" "}
<a href="https://github.com/igvteam/igv.js/wiki" target="_blank" rel="noreferrer">IGV.js</a>{" "}
browser instances upon request to visualize averaged normalized track segments for a given genomic feature.
These averaged tracks are created on the fly by averaging bigWig regions of samples sharing an experimental
treatment and genotype, using our command-line tool:{" "}
<a href="https://github.com/c3g/bw-merge-window"
target="_blank"
rel="noreferrer"><code>bw-merge-window</code></a>.
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