Comments (3)
The splint sequence is fine, but I'm adding splint.fasta
with the exact sequence that was used in the paper. I'm also adding adapter.fasta
that contains the 3' and 5' adapters used in post processing.
I can supply you with a demultiplexing script if you need one. How are you multiplexing your samples?
from c3poa.
Hi,
Thanks a lot for your answer.
If I get it right I will process the ONT data from the 96 samples of B-cells using the splint and adapter you provide. This will generate an output with reads from 96 samples in one single output that will need to be demultiplexed. If you already have a script for those 96 sample I would like to give it a try.
About your question, I don't have my own samples yet, I wanted to try the tool and replicate your results from the paper so I can see the kind of data it outputs (I am actually interested seeing what happens in the percentage of genes with coverage but no isoform detected by Mandalorion II ). Once I am acquainted with the software and data analysis I'll proceed thinking more about the experimental design details.
thanks again!
Mattia
from c3poa.
Sorry this took a while to get to you, but I've added the indexes and the demultiplexing script to the paper directory on the repo. Let me know if you have any other questions and I'll get back to you faster than last time
from c3poa.
Related Issues (20)
- Error in running C3POa.py HOT 5
- DNA splint sequence HOT 1
- C3POa_preprocessing halts when parsing splint blat alignments HOT 7
- question and IndexError: list index out of range HOT 5
- Confusion about the C3POa_preprocessing.py and C3POa_postprocessing.py results ? HOT 3
- how to remove the 3' 5' adapeters or the ployA tail form the postprocessing sequences HOT 1
- Question about -d parameter? HOT 6
- Issues with C3POa.py: cannot execute gonk HOT 15
- Issues when running C3POa.py HOT 10
- C3POa.py: AttributeError: 'tuple' object has no attribute 'append' HOT 17
- Error when running C3POa.py HOT 1
- Error when running C3Poa.py with 10x R2C2 nanopore data HOT 11
- duplicate subread record issue HOT 3
- Error when using bsub HOT 2
- Number of repeats used for consensus HOT 9
- <determine_consensus.py> <pyabpoa.msa_aligner.msa> IndexError: list index out of range
- Very few subreads and consensus reads despite many reads after preprocessing HOT 1
- Calling Consensi Hang HOT 2
- R2C2_C3POa_10X_data analysis
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 c3poa.