Comments (1)
Let me unpack a few things here. Since a fastq record has a quality score per base, tools like NanoFilt and chopper can calculate the mean q score. There are two ways to calculate that score: with (correct) or without (wrong) first change the phred scores to probabilities. See also https://gigabaseorgigabyte.wordpress.com/2017/06/26/averaging-basecall-quality-scores-the-right-way/
NanoFilt and chopper do those things in exactly the same way.
There could be changes to guppy that I am unaware of, but to my knowledge, or at least how it used to be: the difference between the wrong way to calculate and the sequencing_summary is rather big. The difference between the correct calculation and the summary is much smaller, yet it is not identical. This means that there is some aspect of the quality of a read that guppy is aware of and outputs in the sequencing summary file that is not correctly represented in the FASTQ record. So chopper too will not give the same result in that case, but close enough.
from chopper.
Related Issues (20)
- generation of a log file? HOT 6
- Missing libraries of chopper HOT 9
- sequencing_summary.txt feature HOT 1
- error: Found argument 'file.fastq' which wasn't expected, or isn't valid in this context HOT 8
- /lib64/libc.so.6 issue HOT 5
- Filter out reads marked as contaminants? HOT 1
- Cannot Download Chopper HOT 4
- Nanopore barcode/adapter detection HOT 2
- Give minimap more threads when available. HOT 4
- missing ".with_cigar()" in Aligner? HOT 7
- Recommended defaults? HOT 5
- Issue in Installation HOT 7
- Not running on aarch64 HOT 11
- Not working on M2 Mac HOT 6
- Help with --contam parameter HOT 1
- chopper with bam files HOT 1
- Instatlation issue HOT 2
- confuse problem HOT 10
- minimap2 preset for `--contam` HOT 8
- chopper v0.8.0 GLIBC_2.XX not found 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 chopper.