I have just got my bachelor's degree in Biology and I'm learning how to analyse 16s data to interpret the effects of phytobiotic additives on animal productivity through changes in gut microbiota. I'm doing it on my own and it's a whole new world to me. This is why I started to learn how to use QIIME2, after doing some research about the best and easiest softwares/pipelines for beginners (dummies) to learn.
I've been learning how to use qiime for three months now and haven't been able to perform a single analysis because I keep having difficulties and errors on the steps previous to the analysis itself. I wonder, am I just doing it all wrong? Should I try a simpler pipeline (if it even exists)? Or is this just normal difficulty?
I've been having a lot of help form the forum, lots of very patient people have been helping me and I believe it makes a great community to learn. But I wonder if there is something more I could be doing to learn on my own, so I'm here to ask if you people have any recommendation in that matter. Is anybody aware of online courses or something like that, about 16s metagenomics analyses (not necessarily qiime)? I see there are lots of bioinformatics courses, but they don't really get into metagenomics on a deeper and more specific level.
I'm a little worried because I really need to learn how to analyze this data to keep my job, so I highly appreciate your thoughts on the matter!
I hope others chime in here, as I have not used any of these resources so cannot give really valuable input! But I just want to shed light on some existing resources that I know about.
The QIIME 2 website lists some external resources... the Coursera course sounds like maybe what you are looking for (though this might be theory rather than practical, I am not sure): https://docs.qiime2.org/2022.2/supplementary-resources/
Also, in case you have not seen it already, there is a QIIME 2 youtube channel with many videos for different steps. Many or most of these parallel the online tutorials, so you can follow along with the text and video tutorials simultaneously:
Based on this description, it sounds like your issue might be with the data itself (quality? formatting issues?) rather than your own usage of QIIME 2. But this is not clear! Continuing to open up tech support issues on the forum might help get you on the right track...
The learning curve for any bioinformatics tool will be quite steep. One thing that makes QIIME 2 a bit more challenging perhaps is that it is not a pipeline, but rather a flexible software platform that allows you to build your own modular pipelines. So whether using QIIME 2 or another tool, my advice is to be patient and work hard at it — it takes time to master.
Hopefully others can offer more specific resources, also those that they used to learn!
Hi,
I'd highly recommend looking through Coursera's courses. They often have some quite good ones!
And don't lose hope. It was VERY difficult for me in the beginning to understand how QIIME2 and other bioinformatic tools work. The beginning is super difficult and confusing, but keep it up and it will definitely get easier!
If anything, you are more than welcome to reach out for more guidance
I'd also still categorize myself as a beginner, so maybe we can benefit from each other haha.
@CMNZ, thanks! Give it a try now. If it still is not showing up for some reason you can search for it on Coursera, it is called "Gut Check: Exploring Your Microbiome" by Rob Knight and offered by University of Colorado Boulder and University of California San Diego.
