I am new to QIIME2 and have been having a reasonably easy time getting into it thanks to the tutorials, but I have now come to a complication with my data that I have not been able to find any info on in the forum.
I have received fastq data from another group ~1700 files from which I only need ~ 950 based on a condition. I have a metadata file with only the samples I need, but could not find a way to filter the fastq files before working with them in QIIME2. Therefore, I imported and cleaned all samples and got all the way to alpha and beta diversity analysis using the “Moving pictures” tutorial. When I input the code:
qiime diversity core-metrics-phylogenetic
I get an error that ‘There are samples not included in the mapping file. Override this error by using the
ignore_missing_samples argument.’ Of course I knew there were samples missing because my metadata file only includes my samples of interest.
So my questions from this are:
- Can anyone direct me to a fairly straight forward way of selecting my fastq files by sample id before starting in QIIME2?
- How do I add the ignore_missing_samples argument?