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.
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!