Help with using cutadapt

[thermokarst]

Hey there @MAX_MIAO!

@MAX_MIAO

For some reason qiime2 pops up with saying that my .fastq.gz file is not a QIIME archive.

That warning is actually for a really good reason - QIIME archives and Artifacts are a core concept in QIIME 2. If you haven't had a chance to at least peek at the docs, now would be the time - you will save yourself a lot of heartache . I would suggest starting here: Overview of QIIME 2 Plugin Workflows — QIIME 2 2018.6.0 documentation

After you get up to speed there, check out this community tutorial:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin,…

Keep on QIIMEin'!