Comments (2)
Hi @decenwang
The non coding sequences are defined as sequences that are known not to code for a viable receptor containing either a frame shift or a stop codon within the CDR3 region.There is a slight difference with the non productive ones, a term designating any sequence that does not code for a viable receptor (e.g a sequence producing a non folding but in frame receptor). We hypothesize that non coding sequences are non productive, the reverse is a priori not true.
One can find the non coding sequences via sequence alignment of the genomic templates, allowing to find the CDR3 position. There is for now no built in way of doing this via IGoR and you may want to use a different software (for now) for this pre processing step.
As for your third point I'm not sure I understand the question since you abbreviated the original sentence of the paper:
By contrast, V and J gene usage varied moderately but significantly across individuals, and even more across sequencing technologies, suggesting possible primer-dependent biases.
Just to make sure we're on the same page, this sentence means primer-dependent biases are likely because differences are much larger among sequencing technologies than among different individuals using the same technology. Although I agree with your MHC point for productive sequences, please bear in mind that model learning on non coding sequences a priori only reflects statistics from V(D)J recombination and not central/peripheral selection. Differences in gene usage among individuals on models learned on non coding sequences only reflect an individual's V(D)J genes properties (positions, number of copies etc)
Best,
Quentin
from igor.
Hi Quentin, @qmarcou
Thanks for your reply. I think you are right. Anyway I have another idea. primer -dependent bias is innate for primer pairs(bias 1). different sequencing technologies will enlarge this bias(bias 2), and also, templates in individuals are diverse, so the primer pair may find the suitable template(bias 3). However, I have spent more 1 month learning IGoR, but still not keep forward. I will post questions as few as possible. Hopefully, you can respond when you are available.
Thanks a lot!
Best regards,
Decen
from igor.
Related Issues (20)
- File not found when IGoR is installed locally HOT 1
- Errors: python to parse the output results? HOT 2
- Model edge gene choice relations differ HOT 1
- Chain IGoR commands HOT 1
- Missing unknown subargument error for -output HOT 1
- Using the --coverage output subarg HOT 1
- using the --coverage error
- make new database HOT 2
- make check failures but make install worked HOT 1
- Segmentation Fault in -run_demo HOT 5
- Limiting IGoR's CPU usage HOT 1
- Install error HOT 2
- How to get everyone sequence clonotype ?
- the result file foo_indexed_CDR3s.csv HOT 1
- segfault with gcc > 7 HOT 2
- IGoR over-estimating TCR V deletions?
- installation from source
- All 0 output in infer and question about L_thresh
- Remove superfluous IMGT information in TCR beta model parms file
- Undefined reference error during compling
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 igor.