unmapped BAM from Ion 16s Metagenomics Kit using MergeBamAlignment
I have sequenced 16s rRNA from waste water samples using Ion 16s Metagenomics kit. After paired-end sequencing using the machine Ion S5, I have received unmapped BAM files for all samples. Each uBAM contains both forward and reverse reads unaligned. I want to map those unmapped BAM files (uBam --> Bam) using the reference genome (16s gene) before I can convert them to fastq for analysis in QIIME 2.0. However, I am stuck at how to map the ubams? I am new to bioinformatics so any help will be appreciated! Do I have to sort uBAMs in some order before mapping them? I have installed picards but I am not sure which plugin should I sure to get fastq files which I want in the end for QIIME analysis.