arshajii / ema-paper-data Goto Github PK
View Code? Open in Web Editor NEWData and resources for EMA paper
Home Page: http://ema.csail.mit.edu
Data and resources for EMA paper
Home Page: http://ema.csail.mit.edu
Hi,
I ran BWA, LongRanger, and EMA for NA12878 WGS dataset from https://support.10xgenomics.com/genome-exome/datasets/2.1.4/NA12878_WGS_v2, and looking at the challenging regions listed in your notebook:
C4A 6:31965242
AMY1 1:104197843
CYP2D7 22:42537120
It looks like EMA has a higher coverage in those regions, however all those extra alignments are secondary (shaded on the screenshot). I'm wondering if that's an expected picture for EMA? And those secondary alignments could not be resolved via the linked read information? As far as I understand, those secondary alignments will be ignored by variant callers. They look to add up noise in variation, as in this CYP2D6 screenshot (more vertical colored lines at the coverage tracks):
Please, correct me if I'm wrong. I see you evaluated those regions with a more sophisticated strategy by checking against the NA12878 assemblies, so probably I'm not looking at these regions the right way.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.