Comments (2)
When the -strand
option is used for strand-specific data (e.g. ONT direct RNA), the assembly would contain mRNA sequences. Otherwise, the assembly can be a mix of both orientations.
By default, all U's are replaced with T's. You can use the -uracil
option to write U's instead of T's in rnabloom.transcripts.fa
.
FYI: https://github.com/bcgsc/RNA-Bloom?tab=readme-ov-file#b-assemble-nanopore-direct-rna-sequencing-data
from rna-bloom.
Thank you very much!
from rna-bloom.
Related Issues (20)
- Output error message for pooled assembly of single-end reads
- Improve hairpin/palindrome removal in long-read assembly
- Q. Error in extracting unique reads at Stage 3 (Assembling long reads for "rnabloom") HOT 4
- Transcriptome assembly from ONT direct RNA sequencing seems to be incomplete HOT 9
- conda install url not working HOT 1
- Inputting multiple long-read files at once HOT 3
- Java out of memory exception HOT 3
- Exception in thread "main" java.lang.OutOfMemoryError: Java heap space HOT 4
- RNABloom not creating transcriptome files HOT 3
- Errors (reading file and I/O) for one of 9 pooled assemblies HOT 11
- can rnabloom run from stage 3? HOT 2
- Can output be used for DE analysis? HOT 2
- Question about assemble long-read sequencing data with short-read polishing HOT 3
- RAM requirements. What is the minimum? HOT 2
- Consensus transcriptome de novo with multiple samples HOT 1
- reduce redundancy in direct RNA long-read only assembly? HOT 1
- error in assembling ONT DRS long reads HOT 1
- assembling nanopore sequenced bacterial transcriptomes HOT 1
- Improving Sensitivity for Similar Isoform Assembly and Handling PacBio HiFi RNA Reads Without Polishing HOT 3
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 rna-bloom.