Comments (4)
dpryan79
commented on July 22, 2024
I suppose so. Keep in mind, though, that this will end up being per-base (overlapping a CpG) per-read, so the numbers will probably look disturbingly high.
from methyldackel.
avilella
commented on July 22, 2024
Great, thanks.
from methyldackel.
nchernia
commented on July 22, 2024
Similar question: would it be possible to have some kind of alignment report akin to Bismark's, where sequence pairs that are not used are reported? I.e. some alignments are not used due to low MAPQ or low Phred and some supplementary alignments are discarded; it would be nice to know how many of the sequenced read pairs are used for the methylation calls.
from methyldackel.
dpryan79
commented on July 22, 2024
@nchernia I'll see what I can do. The functions that filter reads by MAPQ/flag are buried pretty deep in the code. The phred filtering stuff happens for each base, so I'll try to come up with a reasonably meaningful aggregate value for that.
from methyldackel.
Related Issues (20)
- Stand output HOT 1
- Understanding --minConversionEfficiency argument HOT 1
- Genome browsing from MethylDackel bedGraphCpG file
- per-fragment methylation HOT 2
- mbias result is different between bismark and bwameth output HOT 1
- CURL_OPENSSL conflict with samtools HOT 3
- Installation failure: "bigWig.h: No such file or directory" HOT 1
- Clarification on definition of "unmethylated C" HOT 1
- Coverage of C sites HOT 1
- mbias HOT 1
- Does indel effect the methylation calling or C context determination HOT 1
- Positions in cytosine_report did not match the regions in providing bed file
- about M-bias HOT 1
- Could not repeat a CpG extraction with the same reference file and its index
- Mixed up reads within bam file
- How to index genome file for MethylDackel? HOT 1
- Confused regarding CTOT, CTOB. Are there suggested values? HOT 3
- Issue running MethylDackel extract in parallel mode using minConversionEfficiency
- Question about minimum coverage
- Different CpG calls when using different regions of inclusion for Methyldackel extract
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 methyldackel.