sixvable / q2-dada2-ccs Goto Github PK
View Code? Open in Web Editor NEWmake q2-dada2 support Pacbio CCS
make q2-dada2 support Pacbio CCS
Hello! I replaced the old files (init.py, _denoise.py, plugin_setup.py, run_dada2_ccs.R) to your new files for long reads.
Why can I sill not use the command qiime dada2 denoise-ccs
? Is there other settings? Thank you.
Hello!
In your Usage, you said "Overwrite ... in /path/to/your/conda/envs/qiime2-version/lib/python3.6/site-packages/q2_dada2/ with the file in this repo."
However, in Detail, you said "Changing following files in /path/to/your/conda/envs/qiime2-version/lib/python3.8/site-packages/q2_dada2/"
Which is correct? I know QIIME2-2021.4 is using python 3.8, is it the reason? Thanks!
Hi @sixvable ,
I used this great PR to analyze my pacbio ccs, but around 70% reads were lost after denoise. Is my parameters right ? or is it due to some other issues?
My parameters were:
qiime dada2 denoise-ccs --i-demultiplexed-seqs test.qza --p-min-len 1000 --p-max-len 1800 --o-table test_table.qza --o-representative-sequences test_seq.qza --o-denoising-stats test_stats.qza --p-front AGRGTTTGATYNTGGCTCAG --p-adapter TASGGHTACCTTGTTASGACTT --p-n-threads 0
test_stats.zip
Thanks in advance!
I am using QIIME2/2021.11
via conda
. I installed your edits according to USAGE section of your README.md.
After activating the conda
enironment, when I run :
$ qiime dada2 denoise-css
Error: QIIME 2 plugin 'dada2' has no action 'denoise-css'.
So I tried :
$ qiime dada2 denoise_css
Error: QIIME 2 plugin 'dada2' has no action 'denoise_css'.
Question :
run_dada_ccs.R
directly?Thanks
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.