I previously analysed two datasets in QIIME 2, sequenced in 2018 and analysed in 2019 and 2022. I now want to go back and re-generate some graphs, run the taxonomy again etc. I have my original files including "paired-end-demux-joinged-filtered.qza" and I'm wondering if I should start re-analysis of my datasets from this point, or re-import my FASTQ files all over again. I've been trying all day to work out what format my files are in and getting confused over PHRED offsets and manifests Has the process changed since 2019? Has it been improved such that it would help to start from scratch again? Help me please!
The answer to this depends on what your end goal is - if you'll need to include this analysis in a publication, it's probably a good idea to re-run everything using the same (newer) version of QIIME 2. But if your goal is to just do some additional exploration or revisit what you did previously (essentially without any immediate publication goals in mind), you shouldn't necessarily have to re-import your raw data or re-create any artifacts.
If you have QIIME 2 Artifacts (ie .qza files), you should be able to see what the file format is by running qiime tools peek FILE on the particular artifact, with FILE corresponding to the relevant artifact's filename.
Many things certainly have changed since 2019, but you should still be able to view and manipulate artifacts you created from that time in the current version of QIIME 2. If you are running into a specific error message, feel free to share that here (along with the exact command you ran) and we can take a closer look!
Has the process changed since 2019? Has it been improved such that it would help to start from scratch again? Help me please!
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