Selecting samples from separate sequencing runs

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!

If you have 3 separate fastq files, the implication is that these are not demultiplexed yet. When you demultiplex, merely omit the samples you do not want from your sample metadata file. Only the samples listed in the sample metadata file will be retained.

If you plan to use dada2, do not merge these fastqs. Demultiplex and denoise separately, then merge the feature tables.


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