Comments (3)
Sorry this is overtuned for my setup; I keep an environmental variable pointing to reference genome files. You should be able to dodge this by providing the genome FASTA file with -f. If it's still breaking on the default, just change it to something benign.
I may be overinterpreting your command, but you'll want to be very thoughtful using this program for CLIP-seq modeling. If you just provide large genome blocks like I do for DNase, ATAC, ChIP, and CAGE, you'll be asking the model to learn gene transcript definitions as well as the RNA binding protein sites. I expect that'll be too hard. That's why I focused on CAGE rather than RNA-seq for gene expression. You can provide smaller sequences and make the program behave more like Basset, but I haven't tested that thoroughly. I also haven't tested variable length sequences like you might want for RNA.
from basenji.
i have provided the fasta file using -f but still its breaking, I think i will change the default. Also i am actually looking for RBP binding sites from the CLIP data(as i dont have a CAGE data for this). So my plan was to preprocess the bam, train the sequences and predict motifs. Do you think this approach make sense??
from basenji.
It might work, but you'd likely fit much better models if it better understood the isoform structure of the genes. E.g. I would assemble the training set as RNA sequences annotated with the CLIP coverage or some transformation of it. But in that case, you have variable length sequences, and I don't think Basenji will work out of the box. Maybe you can choose a length that covers most genes and pad the shorter transcripts.
from basenji.
Related Issues (20)
- Problem with calculating the target based on the gene sequence HOT 1
- None in maps HOT 4
- .hic
- Expose 'raw' as an argument? HOT 2
- Black list HOT 6
- handling blacklist\unmappable HOT 1
- basenji_data_align.py train/test/validation splits HOT 2
- How to set different GPU No. ? HOT 2
- Stable environment configuration HOT 1
- How to convert the keras model to a basenji model HOT 1
- Pre-process tutorial file not working HOT 2
- tutorial training with --sample 0.05 HOT 3
- Making Akita predictions for different bin size HOT 2
- Attention layer HOT 4
- Seeking Guidance on bam_cov.py Parameters HOT 2
- When using Akita for single-cell prediction on the HCT116 cell line, the Pearson correlation coefficient is much lower. HOT 8
- Akita: Loading weights for newer models results in mismatch HOT 2
- Issue with final matrix?
- OOM issue
- Reproduce the Enformer's input sequences split 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 basenji.