I have fastq files (forward and reverse reads) of different samples of nifH gene generated by Illumina MiSeq platform. I need to find bacterial community and distances between groups. Therefore, please suggest if I can use qiime in this way.
Though I’ve never used the nifH marker gene myself, I can’t imagine why you shouldn’t be able to follow most, if not all, the typical QIIME2 workflows for this. Have you tried looking through one of the many available tutorials to see if what you are looking for is not already described there? For example the Moving Pictures tutorial there shows a rather complete process and it does show you how to calculate distances between groups (beta diversity).
In Moving Pictures tutorial needs several files such as unweighted_unifrac_distance_matrix.qza, faith_pd_vector.qza etc to calculate diversity. However, I need to follow the initial process to generate these files. In this tutorial I can not find the steps how to work on fastq files and which is the references databases that I should use. SILVA?
Please have a careful look at the Moving Pictures tutorial again, right from the beginning… It starts with downloading raw .fastq files and step by step shows how to go about developing all those intermediary files such as distance-matrix etc for downstream use. In your case you already have the .fastq files so you wouldn’t be downloading anything. Your importing step might differ than the Moving Pictures tutorial, see the importing tutorial to find the method that matches your file format. Once you have your fastq files imported into QIIME 2, then you can resume following along the Moving Pictures tutorial which also has a step that shows when you would use a reference databases (example Greengenes or Silva).
Please read the tutorials carefully and let us know if you run into any specific problems.
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