Hello everyone,
I have 3 separate fastq files (generated from 3 separate Illumina sequencing runs) and I need to select only some of the samples in these runs prior to running them on the QIIME pipeline. I have the Sample ID’s for the specific samples I want to keep (I want to select 200 samples out of 500 that were run).
At what stage and how can I select these samples for running on the QIIME2 pipeline? Do I have to merge the three sequencing runs together and then filter out the samples that I want to discard? Or do I have to select the samples that I want to keep prior to starting?
Thank you in advance for your help!