importing UBAM files to QIIME 2.0

Question

[osamashehzad.786]

Hello everyone!

I am new to fields of bioinformatics and trying to learn it as much as possible. I used iontorrent to sequence 16s rRNA data to analyze microbiome diversity in drainage water. I am using QIIME 2.0 to perform the metagenomics analysis however I am stuck at preprocessing. I only have UBAM sequence files from iontorrent which I am unable to import into QIIME 2.0 (which normally processes fastq). How can I resolve this problem?

I have seen many solutions but each have their limitations so I am not sure what is best way to solve this problem without losing any of the sequencing data before I feed it into QIIME.

Answer 1

[Istvan Albert]

Convert your unaligned BAM file to FASTQ

samtools fastq bamfile