I am very glad to see so many great questions on the forum! You are thinking about the HPC and Nephele pipelines and how we can troubleshoot to get results and analyze the data.
Remember that we have two powerful tools: Nephele and the HPC (QIIME2/DADA2) that we can use to analyze the 16S and ITS data we have as well as KBase for the Nephele data from the compost sample. All data are shared on this Google Drive folder.
Trimming and filtering are important steps that we must not overlook. After you trim with Nephele, for example, run your trimmed samples again to confirm it worked. If you can, share your results and what you did.
A couple of you have started annotating our third article found here. This study reveals changes over time with respect to an event we all probably heard about!
Please review podcast scripts and let me know if I need to assign another script to you, as the system may have given you no script or your own since we worked in teams!
Take care!
CG
