Comments (1)
That doesn't really surprise me, as much of the TCGA cohort is low-depth sequencing (by modern standards).
See Figure 5 for for an illustration of how low sequencing depth increases sampling error and makes it very difficult to infer clonality accurately:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669575/
One decent sanity check is to plot the data and ask yourself whether you could call clusters by eye that are being missed, or whether the data is really quite noisy/dispersed
from sciclone.
Related Issues (20)
- Where to download these 3 input files? HOT 1
- 2D plot doesn't show all clusters HOT 10
- Question about 3d plot
- sc.plot2dWithMargins Error HOT 3
- Backfilling ref and alt depth for variants only detected in one sample of multi-sample clustering HOT 1
- How to classify subclone frome sciClone result ? HOT 4
- Input purity dara HOT 1
- Can I still use sciclone? HOT 4
- Question about sciclone output HOT 1
- Topological tumour samples HOT 1
- How to get five columns of vaf data for sciclone HOT 1
- Structural variants as input to sciclone HOT 3
- can't do clustering - no copy number 2 regions to operate on in sample 15 HOT 2
- Application on targeted NGS data HOT 1
- Cannot install NORMT3 HOT 4
- Error in xtfrm.data.frame(x) HOT 4
- How to distinguish between clones and subclones HOT 2
- Question about the result of sciclone HOT 2
- Does sequencing depth matter? HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from sciclone.