Hi everyone,
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.