Comments (4)
Magdoll
commented on June 7, 2024
Hi @aarzalluz ,
This error is coming from trying to parse the ORF information produced by GENEMARK. It could be an edge case that I did not handle well (or maybe some issue with the ORF fasta file).
Is it possible to share this data confidentially for debugging?
-Liz
from sqanti2.
aarzalluz
commented on June 7, 2024
Sure, I can share the input fasta and FL counts as well as the reference genome/annotation version I'm using -do you think that would be enough for you to replicate the error?
Ángeles
from sqanti2.
Magdoll
commented on June 7, 2024
Hi @aarzalluz yes that will work. Please coordinate with me through email at [email protected]. I can give you a secure place to upload data.
from sqanti2.
aarzalluz
commented on June 7, 2024
Hi, Liz
I realized I had made an error when mapping -sorry about that! SQANTI2 is working now regarding ORF prediction. I'll close the issue.
from sqanti2.
Related Issues (20)
- input isoforms.fasta for chain_samples.py HOT 4
- isoform map to scaffold which without reference gene HOT 1
- Assertion Error HOT 7
- gene_id annotation HOT 2
- Possible error from input gff files instead of fasta/fastq/gtf files HOT 10
- Tamma Collapse for 5' cap selected samples HOT 1
- sqanti2_qc.py fails with assertion error HOT 6
- Isoform class transcript distribution versus rarefaction curve HOT 1
- How to utilize sqanti2 classification result for genome optimizaion? HOT 1
- python 3.7 bx-python error HOT 1
- About adapting SQANTI2 to process transcripts from nanopore cDNA sequencing HOT 2
- Problem running with cage_peak HOT 2
- _corrected.gtf file without transcript line HOT 4
- FileNotFoundError: missing refAnnotation_***.genePred file? HOT 3
- Error with sqanti_qc2.py command HOT 4
- sqanti_filter.py HOT 4
- issue with python=3.7
- Gene_IDs in GTFs HOT 3
- Recurring perl errors - gmst.pl HOT 7
- error using GFF or converted GTF 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 sqanti2.