I got currently working on a MiSeq Dataset 16S which does not have a separate barcode file in the folder. I know that the barcode information are already in the sequence file as the name of each files are in the following format:
There are 145 of such files. I have actually browsed through some of the previous suggestions as mentioned in the website (Problems with fastq files paired end without barcode file). But still not able to find my required solution.
I am actually trying to create qza file extension using all the sequence data in the folder. It will be really helpful for me to anyone share some suggestions.
Importing different data types is described in the QIIME2 tutorials page — in particular, it looks like you have Casava 1.8 paired-end demultiplexed fastq files, which you can import as described here.
You would place all of these files (and nothing else) in a single folder, then import that entire folder as a QZA as described in that tutorial.
Thank you for the suggestion. Just have a query can I keep any other file formats like .txt or .csv files along with fastq.gz files in that same folder. Those files are just summary of the barcode info.
I think any non-fastq file may cause an error while importing, because QIIME2 does not expect these file types with this command. But I am not certain — text files may be okay. If in doubt, give it a try and see what happens!
I was able to generate the qza files using the dataset. Thank you for your help. But can you share some suggestions how I can view the contents inside the qza files.
A QZA is really just a zipped archive containing specific files that QIIME2 recognizes. So you can simply unzip a QZA to look inside, but the proper way to examine the contents is to use:
qiime tools export
See this tutorial for more details.
There are specific methods for viewing and summarizing different QZA contents, depending on the file type. This tutorial covers most of the basic viewers — any method called
summarize is going to be a method for viewing the contents of a QZA in a more direct manner than unzipping/exporting the file.
It sounds like you are just getting started in QIIME2. You should check out our getting started guide and try out some of the tutorials to get a hang of how QIIME2 works, particularly importing/exporting and working with QZA files.
I hope that helps!
Thank you for your help. I did go through some of the materials and they are helpful.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.