sixvable / q2-dada2-ccs Goto Github PK

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 :

1. How do I get your plugin to work? Do I just run run_dada_ccs.R directly?

Thanks

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.