If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
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.