Hello to all.
First time writing on the forum and trying to analyze with qiime2 data generated with ion Torrent after using 16s Metagenomics kit.
As most of you will know, the 16s metagenomics kit amplifies 7 different regions of the 16S gene into 6 amplicons. So after downloading my data I have a FASTQ with a mix of all the single-end reads of all the diferent regions.
In order to compare my data with bibliography, I want to analyze only the sequences that correspond to the v3 region, Can anyone give me any clues to separate the sequences according to the region from which they come from? Maybe one of you has done it before.
I´m thinking on trying to separate them by aligning with the whole 16s gene as reference, or an anyone give me any clues to separate the sequences according to the region from which they come from? maybe one of you has done it before.
I can think of trying to separate them by aligning them with the whole 16s gene as a reference or try to filter them with the used primers but I do not have Bioinformatic experience and I dont know programs, plugins or resources to do this job.
Thanks to all