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cduvallet / q2-perc-norm

QIIME2 plugin for percentile normalization to correct for batch effects in microbiome case-control studies
BSD 3-Clause "New" or "Revised" License
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Steps for downstream analyses in qiime2 #8

Closed Alenap26 closed 1 year ago

Alenap26 commented 1 year ago

Hello, thank you for providing this package. I'm trying to integrate it into a pipeline that utilizes qiime2. I'm encountering difficulties in integrating the output type (FeatureTable[PercentileNormalized]) generated by q2-perc-norm. I need to incorporate this output into the subsequent pipeline command as input.table:

qiime diversity core-metrics-phylogenetic --i-phylogeny {input.tree} --i-table {input.table} etc..

Could you suggest the steps to use the output of q2-perc-norm in downstream analyses?

cduvallet commented 1 year ago

Hi @Alenap26 - please see this forum post with an answer to your question: https://forum.qiime2.org/t/q2-perc-norm-questions/9171

If you have additional questions on how to use the plugin, please use the qiime 2 forum. (This repo is for reporting issues/bugs with the code)