Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.