Comments (3)
That GFF3 file seems badly formatted, the essential attribute "Parent" is spelled "PARENT" which is incorrect (these attributes are case sensitive according to the GFF3 specification).
Simply transforming the file with something like perl -pe 's/(NAME|PARENT)=/\L\u$1=/g'
should fix this. I suspect TopHat just failed silently at loading that annotation (i.e. no transcript features were actually loaded).
from cufflinks.
Sounds like it's a bad GFF file (shame on ensembl...) but I don't think a segfault is the best response.
Perhaps an error message with the location in the input would head off this kind of question in the future?
from cufflinks.
I fully agree. I have added some code checking for situations like this, hopefully it's going to make its way in to the next release.
from cufflinks.
Related Issues (20)
- Please use std::fabs instead of just fabs in C++ to avoid conflicts
- The https version of cufflinks website looks broken
- Please add the corresponding ifdef for the code meant only for MinGW
- -m64 breaks build on architectures other than amd64
- configure error: We could not detect the bam libraries
- error: reference to 'thread' is ambiguous HOT 1
- Correlation between replicates
- Nondeterministic segfault on OSX
- 0 ReadHits still live
- Intron not within scaffold warnings HOT 1
- license clarification
- Cuffmerge:ValueError: can't have unbuffered text I/O HOT 5
- cuffmerge
- Cuffmerge GTF error
- Performance data of cufflinks in computing speed.
- Cufflinks - Inconsistent Results for SAM/BAM File Sorted by Reference Position
- cuffdiff error: number of labels must match number of conditions
- multithreading
- # coverage and -g and -G
- Unusual behavior of cufflinks when a colon is present in the contig names
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 cufflinks.