Comments (3)
By default, the position reported in the pos column refers to the first nucleotide of the kmer. You can adjust which position relative to the kmer is reported by changing the context parameter. For RNA002 data, 0 refers to the first position of the kmer (default behavior), 2 would refer to the middle position in the kmer, and 4 would be the final position of the kmer, and everything in between.
from nanocompore.
Hi, please can you clarify more and share the command to change the position? is it this --sequence_context {0,1,2,3,4}]
what does 3 means?
Is the red circle what you mean by position? I want to detect the difference in charge intensity between nucleoside analogues and natural nucleosides. Specifically, I'd like to examine the intensity of the nucleotide at the central positions. Is this possible using a nanocompore?? Thanks in advance
![Screenshot 2024-07-08 at 21 58 01](https://private-user-images.githubusercontent.com/52241597/346694143-fd2e9769-fe32-4a8a-8c68-4675a4892f6b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.PFcHh0MrKpoDdNjobtVH2LulaBWsNPBRmBOlgb18roc)
from nanocompore.
Hi @g-s-2018,
Because of the nature of the nanopore, 5 (RNA002) or 9 (RNA004) nucleotides are in the sensitive region of the nanopore at any given moment. The ionic current for a particular position is the result of multiple nucleotides occupying the sensitive region of the nanopore which we refer to as a kmer. We can assign to ionic current from a kmer to a particular position in several ways.
Generally (but not always), the nucleotides exert the largest impact on the ionic current when they are in the central position of the kmer, which is closest to the most sensitive region of the nanopore. So we can model this by converting the physical properties of the kmer into a single position based on the index value of the kmer. When 0 is used (default behavior), this means that we are using the position of the first nucleotide in the kmer to assign all the ionic current for the entire kmer. This usually means that the actual modified nucleotide is 2 nucleotides downstream of the reference position for the modification.
So in your example GAGGT, if you used the default parameters for nanocompore, the most probable modified nucleotide is the central G, but depending on the nature of the modification it can be off by a position or two.
When using the default parameters, I recommend looking at the ionic current for the kmers 2 positions upstream through 3 positions downstream. This will represent all the kmers where the modified kmer is likely to pass through the pore and you should see an effect in at least one of those, usually more.
If the nucleoside analogs are randomly incorporated throughout the strand, nanocompore is not the ideal tool to solve this problem, because it relies on several molecules in the same position to all have differences in their ionic current profiles compared to the control sample. If the nucleosides are randomly dispersed, the signal will be rather difficult for nanocompore to detect. But if the nucleoside analogs are incorporated at a known or the same position, then nanocompore should be able to detect the ionic current differences.
If you're mainly interested in the central position of the kmer, then I recommend changing the --context parameter to 2 instead of 0. This will assign the ionic current for a kmer to the position of the central nucleotide (RNA002) instead of the first position.
We're working on a nanocompore update to RNA004, but it is going slower than anticipated.
I hope that this helps, and if anything is unclear don't hesitate to ask.
Cheers,
Logan
from nanocompore.
Related Issues (20)
- plot position is giving an error HOT 5
- cluster_counts interpretation HOT 1
- Issues on reproducing the synthetic oligo results from the nanocompore paper HOT 3
- Request for demo data & getting ValueError: 'read_name' is not in list when running nanocompore eventalign_collapse with nanopolishComp data HOT 11
- nanocompore to be used for SHAPEseq data HOT 1
- returns numpy error while intsalling nanocompore on Ubuntu 22.04 HOT 2
- miCLIP dataset HOT 2
- A question about the result HOT 1
- nanocompore-sampcomp-References found in index: 0 HOT 2
- nanocompore sampcomp output question. HOT 5
- Problems with save_to_bed. And questions with bed file annotation HOT 1
- SystemError: null argument to internal routine HOT 7
- Nanocompore SampComp stuck at 0% HOT 8
- Steps to make Nanocompore Work HOT 1
- db type is dbm.gnu, but the module is not available HOT 4
- numpy' has no attribute 'float'. HOT 3
- Parameters recommendation to analyse SARS-CoV-2 data generated us Oxford Nanopore DRS protocol HOT 2
- sharkfin plot too many data points and difficult to visualize HOT 1
- Direction of change in methylation HOT 1
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 nanocompore.