preprocessing raw sequence data in a UBAM file from IonTorrent 16S Metagenomics kit
I have raw, paired-end sequence data in a UBAM (unmapped) file after sequencing 16S gene from water samples. The UBAM file contains both forward and reverse reads but unjoined. How can I do the following:
1) Map UBAM to a reference genome so that I will have an aligned, paired-end mapped BAM file? I heard you can use picard but which function to use, I am very unsure.
2) Prepare that BAM file for analysis in QIIME 2.0 by converting it to fastq? I believe I can use samtools to convert BAM to FASTQ but I want to get your advice.
These may be silly questions but I am new to bioinformatics so any help will be appreciated!