I am familiar with QIIME1 but relatively new with QIIME2. I have gotten my raw file in the past from a facility in the CASAVA pair ended demultiplexed format and I had no problem analyzing those files with both versions of qiime.
I am now conducting an investigation of public data available in the SRA archive and I am having a time importing the raw data as QIIME2 artifacts.
I have downloaded different projects (prefetch and fastq-dump commands in the SRA toolkit) and I don’t think they are demultiplexed (?) so I guess I have two questions:
- How do I evaluate which what to specify in the --type option of the import script?specifically how do I tell what type of data I have?
- would I be better off just demultiplexing the data first and then rename everything in the casava format? is that even an option? I looked around the forum and maybe the manifest format would be the option?
I am running qiime2-2020.6