Problem using feature table group

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

  1. 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
  2. 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)

I can visualize the artifact now but still what is --p-mode usage in my case

Hi @Tahseen_Abbas,

You need to go back to the feature table before you merged the two runs to rename them. Here’s even a nifty new command, qiime feature-table rename-ids, that will let you rename the samples and is faster than the grouping command.

Best,
Justine