Comments (2)
Dear Woody,
Thanks for your feedbacks. One thing you can do is to check if the loops you detect correspond to groups already established, for example you could compute the proportion of your detected loops that overlap cohesin peaks. I don't know if your cells are synchronized but in interphase, you should see an enrichment of your detected loops in cohesin or CTCF binding sites.
from chromosight.
Dear axelcournac,
Thank you for your quick and detailed response! Fortunately, my bulk data are synchronized in G1 so I definitely will try the methods you provided :)
Could you please give some further instructions on which parameters (perc-zero, perc-undetected, pearson...) should be changed but not ruin the precision?(As I have mentioned I have low sequencing depth...)
My initial attempt implies that increasing perc-zero can more significantly increase the loop detected(from 300 to 600 for chr1), and a lower pearson is also the case. And different resolutions(5k,10k,20k) with the same default parameters can call loops of different scale(5k calls more diagonal loops than 10k and 20k).
And I have an even smaller Micro-C dataset of 10M contacts. Do you think I can apply chromosight to de novo call loop on it? I see previous answers that suggest ML-enhanced signal as input, but enhanced signals are just not that real, right?
In a word, thank you so much for you kindness and patience!
Best wishes!
Woody
from chromosight.
Related Issues (20)
- Different score values between chromosight detect and chromosight quantify on borders pattern HOT 2
- How to compare loops of Hi-C from different conditions like DEG in RNA-Seq? HOT 4
- Questions about resolution in loop json file HOT 2
- Chromosight for single-cell Hi-C HOT 8
- Point and click mode HOT 8
- Different number of patterns for the same Hi-C matrix HOT 3
- How to evaluate the detected loops? HOT 4
- Different number of loops on GM12878 Hi-C map HOT 2
- chromosight detects hairpin, the numer is too large HOT 1
- Can chromosight detect loops based on restriction fragments level (1f, 2f, etc) HI-C matrix. HOT 2
- Bus error in chromosight quantify HOT 2
- How does Chromosight compute the Pearson correlation ? HOT 2
- Is there a way to use multiresolution .mcool files directly? HOT 1
- Where do these kernels come from? HOT 5
- Loop score calculation HOT 4
- Pattern = TAD? HOT 1
- Recommend parameters of borders detect HOT 1
- HicMatrix generated cool file not supported - possible solution HOT 6
- Handle variable bin size
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 chromosight.