Comments (2)
Itβ can run in sqanti_qc.py
python /disk/luping/tools/SQANTI_Source_Code/sqanti_qc.py -t 15 -g ISO-fusion.collapsed.gtf Fusarium_graminearum.RR1.41.chr.gtf ph1.fasta
**** Running SQANTI...
**** Parsing provided files...
Skipping aligning of sequences because gtf file was provided.
Indels will be not calculated since you ran SQANTI without alignment step (SQANTI with gtf format as transcriptome input).
**** Predicting ORF sequences...
**** Parsing Reference Transcriptome...
**** Parsing Isoforms...
Splice Junction Coverage files not provided.
**** Performing Classification of Isoforms...
Number of classified isoforms 55567
**** RT-switching computation...
Full-length read abundance files not provided.
Isoforms expression files not provided.
**** Writing output files...
**** Generating SQANTI report...
Warning: Ignoring unknown aesthetics: stat
null device
1
[1] "SQANTI report successfully generated!"
287.92987895
from sqanti2.
Hi,
You need to supply the --aligner_choice=minimap2
option for sqanti_qc2.py
.
--Liz
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
π 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. πππ
-
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 β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from sqanti2.