Hey there,
Is there a way to remove singletons from feature tables?
Thanks!
–Lorinda
Hey there,
Is there a way to remove singletons from feature tables?
Thanks!
–Lorinda
Hi @Lorinda,
Yes! You are looking for feature-table filter-features
.
You would do something like:
qiime feature-table filter-features \
--i-table table.qza \
--p-min-frequency 2 \
--o-filtered-table feature-frequency-filtered-table.qza
I hope that helps!
@Nicholas_Bokulich Yes thank you! I guess I probably should have been able to find this on my own… Thanks for your time
Wouldn't you have to set the min-frequency to 2 in order to remove all features with only 1 read?
Thanks @Stream_biofilm for catching this! You are correct — I have edited the original post.
I had that problem too!
Eventually I found this page listing all the qiime 2 'scripts'
https://docs.qiime2.org/2017.11/plugins/available/
I hope that help,
Colin
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.