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extracting forward and reverse reads from uBAM file

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.


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