I am new to QIIME2, I installed ubuntu and anaconda and qiime2.I am analyzing 16S rRNA data amplified with 341F and 806R targeting the v3v4 region of the gene.
But the commands are so complicated to me (rocket science), don't know which line to choose.
I stared with making a directory and imported my fastq gz files from a google drive link and got lost after that.
Any help with the line command needed to be followed would be greatly appreciated.
the https://docs.qiime2.org/ is like Chinese to me
Thank you in advance
Welcome to the forum!
It's really difficult to determine how to help you right now, because we don't understand where specifically you're having trouble. "Any help" doesn't tell us what format your files are in, which might affect importing, or what piece of he commands you're struggling with.
If this your first time working with the command line, I'd recommend going through a general command line primer, like the ones by The Software Carpentry introduction and an introduction by Joslynn Lee. However, these will get you comfortable with the command line but not necessarily the QIIME 2 specific command structure. If the terminal is too intimidating (we've all bee there), you might also look at other interfaces/APIs, like q2-studio.
If the issue is qiime2 specific, you might want to watch the youtube series from a recent workshop which walk you through the platform and work through the Parkinson's mouse tutorial as a real data example.
If this is your first analysis, I would recommend getting familiar with the software on a well behaved set of data like a tutorial dataset before you venture into the wilds of your analysis. There are specific things that will depend on your data, but it should give you a general overview.