Importing fastq file for analysis

I’m new to the software (using qiime2 studio) and am doing a research based internship on bioinformatics. I have a collection of files (.full.fastq, .pr.fastq, mapping.txt,…) from a separate lab that sequenced fecal and cecal samples from 2 different birds. I’m having trouble teaching myself the steps, and would love some guidance through posts or pvt msg from someone. I can give more information as needed, but had to start my questions somewhere. I have prior comp sci experience, but this is a whole new adventure for me.

Thank you =]

Hi @Chozinentropy,

Welcome to the :qiime2: forum! (And microbiome analysis!)

I have good news and bad news for you.

The bad news is that we can't help you sort out the specific files because every sequencing center, lab, and sometimes person, handles them slightly differently. The best way to figure out which files you should be using is to talk to the group who generated the files/your supervisor. (Plus, I contend that one of a bioinformaticians most important relationships is with their data generation group.)

Okay, the good news: we have pretty good documentation and tutorials for the QIIME 2.

So, once you figured out what the files are, I recommend the importing data tutorial to figure out how to get it into QIIME. If it's demultiplexed, I would suggest the manifest format. If it's multiplexed, you'll want to look at the demux and/or cutadapt plugins.

I would also/in parallel recommend looking through the workflow tutorials. I like the PD mice workflow tutorial best, but moving pictures is a good option, and both present similar analyses.

Also, feel free to come ask questions here as they come up, as well!



Update: I have managed to split the .full.fastq file into the 4 sample data sets (.fastq).

Okay, so based on that, I’d say you potentially have demultiplexed samples, and go from there.


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