Filtering samples from sequencing run before running DADA2

dada2

#1

Hi everyone,

I have a total of 192 samples that were run on a MiSeq sequencer. I would like to filter the samples and only retain 137 samples before running DADA2.

Is this possible? The other samples are from a collaborator and I don’t want to include them in my analysis. I know that they can be filtered out later on when I have a table but won’t this affect my results? I would like to exclude them before running through the QIIME2 pipeline.

Thank you for your help!


(Justine) #2

Hi @thextramile,

This probably depends on how you do your demuliplexing. If they’re already demultiplexed, I’d use the manifest import and only list the filenames/paths you want.

Best,
Justine


#3

Thanks for your prompt reply @jwdebelius :blush: I need to demultiplex the files. I’m starting with 3 fastq files (barcodes, forward and reverse reads). I then gzip them and import them using qiime tools import (EMPPairedEndSequences).

The following step is to demultiplex the read files based on sample names. Do you think that it’s possible to include a mapping file here that specifies the samples that I want to keep?


(Justine) #4

Hi @thextramile,

Its certainly worth trying! I think if you only pass the barcodes you want to use, it should work.

Best,
Justine


#5

It worked - thank you!