Hello, I also have a bam file output from ion torrent 16s metagenomic kit, but I’m confused about downstream analysis. I want to use qiime2, I am confused about if I have to transform to fastq first. Is this kit given paired end reads? I am pretty new in this analysis
Yes, you will have to transform your bam files into fastq before they can be imported into qiime2. You can always try asking your sequencing facility if they have fastq files instead or recommend something that works with their output. If you have no luck there you can always search for one of the many tools out there dedicated to this. For example: bedtools here or picard here., though I have never personally used either of these tools.