I m trying to follow the new user tutorial and I have performed many steps of tutorial as well. One thing I am unable to understand is where to get metadata file for my data ? I have only fastq and fna files.
You data should come with metadata or should be linked with some kind of metadata. This might include the sample type (fecal, oral, soil, etc) or the source (person 1, dog 1, person 2, etc). Its information that was (hopefully) collected at the same time as the samples. If you don’t have metadata, you’re very limited in your ability to analyze your microbial community since you have no way to group your data or test your hypothesis.
@jwdebelius Thanks for your help.
I have a file which looks like this.
These names do have some meaning. but the sample metadata also contain other information columns like Bar code Sequence and Primer Sequence etc. and I dont have them. so how to proceed ?
So, this is another change from QIIME 1: no more hard requirements for metadata. The metadata tutorial talks about this better than I can. The jist is that you no longer need
BarcodeSequence (or an equilivant column) unless you’re using it for demultiplexing; Im guessing that if you don’t have it you probably already have demultiplexed samples but otherwise, talk to your sequencing center/wetlab team.
Got It. One more thing I need to know that is it necessary to have data from different sources ? as I have 4 fastq files from 4 different soil samples.
It’s necessary to have a set of samples that can answer your hypothesis. There are limitations to the statistical tests in QIIME that have discussed a fair bit on the forum. Here’s a recent discussion, although it can be helpful to search for others.
In general, I would expect a comparison of two samples per group to be underpowered to make statistically meaningful interpretation.
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