Comments (4)
Usually using supplementary and secondary alignment can cause methylation reading errors. MethPhaser will output errors if you use secondary and supplementary alignments.
from methphaser.
Yep, I agree. But my point is about re-introducing those reads AFTER running methphaser before assembling.
from methphaser.
I would advise not to do that because MethPhaser flip the phaseblocks and flip the reads' haplotype assignments when it finds the relation between two neighbor phaseblocks are flipped. i.e., HP1 in phaseblock 1 is the same to HP2 in phaseblock2. Reintroducing those reads might be not optimal.
from methphaser.
Thanks for explaining, I see your point!
from methphaser.
Related Issues (12)
- IndexError: list index out of range HOT 5
- Duplicated and missing entries in .methphased.vcf HOT 6
- some block have only one SNP HOT 2
- Possible no caught error for single blocks
- Empty output vcf and bam HOT 4
- IndexError: list index out of range
- Two warning messages appear HOT 2
- The total size of the output bam file has decreased
- KeyError: ('C', 1, 'm') HOT 25
- Error when running meth_phaser_parallel HOT 3
- [E::bam_parse_basemod] MM tag refers to bases beyond sequence length HOT 17
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 methphaser.