Comments (4)
How does your input data look? What is the average read length?
This error can happen, when the ORF extraction module was not able to extract a single ORF, due to the minimum ORF cutoff.
If your reads are only 100 residues long, then you should use an lower cutoff (something like --min-length 30
).
from plass.
We intend to fix this in the next release by taking always a fraction of the sequence length as cutoff for the orf extraction.
from plass.
Thanks, that got me a lot further. The reads were only 1x75bp. I selected minimum ORF --min-length 20
and got a lot further.
Thanks!
from plass.
The sensitivity of Plass can suffer from such short reads because we compute an e-value for the overlap. It is difficult to be significant which such short fragments.
from plass.
Related Issues (20)
- map of input sequences to assembled sequence
- missing handling of small number of input reads HOT 7
- Error running mpi job with class HOT 1
- Use Plass for euk metagenomics data HOT 2
- The output file is empty HOT 1
- Segmentation fault translatenucs HOT 2
- Some Issues about the length of protein sequences HOT 2
- Empty (len:0) sequences in plass output HOT 4
- Issue with Docker image soedinglab/plass:latest HOT 2
- Use PLASS in metatranscriptomic data HOT 5
- Update MMseqs2 submodule
- Install issues HOT 6
- Paired read prediction - mergereads failed HOT 3
- Quantification
- High level of duplicated protein sequences HOT 1
- mmseqs extractorfs can tranlate orfs but CLI does not allow to specify tranlation table HOT 2
- general question to gauge dev opinion/advice on selecting proteins for gene phylogenies HOT 2
- Quality trimming reads? HOT 2
- Alternative codon table HOT 2
- Insights needed for comparison with other assemblers 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 plass.