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.
extracting forward and reverse reads from uBAM file
I am using Ion 16s Metagenomics kit to perform microbiome analysis in wastewater. After performing paired-end sequencing, I have been given raw reads in a UBAM file which contains both forward and reverse reads (unaligned). I used samtools to convert the UBAM into FASTQ (because QIIME 2.0 doesn't accept UBAM). However, I was unable to get both forward and reverse reads. I used the following command to convert ubam to fastq
samtools fastq -0 out.fastq input.ubam which gives me only one output fastq file whereas I need two fastq (one containing forward and other containing reverse reads).
Please help! I am stuck.