Hi
I had metagenome data run in 2 batches(143 samples each,same sample run in both runs).Later in the analysis i realised that while merging the data from both runs (using 'sum') i had not mentioned the batch wise samples as unique id's so can't visualise the batch effect.Now i have used feature table group to relpace my sample ids with sampleid_batchinfo using following command
qiime feature-table group --i-table table_270_190.qza --p-axis sample --m-metadata-file metadata_batchinfo.tsv --m-metadata-column Batch --p-mode 'mean-ceiling' --o-grouped-table feb_table_270_190_grouped.qza
My query is
- Do i have to use this command on both of my denoised runs data (replacing sample id with sample id_batchinfo)
2)I couldn't get the use of --p-mode here bcz i don't want to merge the data within my single run - Also, the way table artifacts can be visualized in QIIME View,i am not able to visualize the output in this case
feb_table_270_190_grouped.qza (276 KB)