Importing ubam files into qiime

Thanks for the details @osaama.shehzad! Here’s what I’d recommend trying:

  1. Convert the UBAM files to FASTQ files using an external program. You should end up with two FASTQ files: one file for the forward reads and one file for the reverse reads.

  2. Import the multiplexed FASTQ files and use the q2-cutadapt plugin to demultiplex the sequences. You’ll also want to use that plugin to remove any other sequencing artifacts such as primers and adapters (the demultiplexing will remove the barcodes for you). Check out the q2-cutadapt community tutorial for examples of how to import, demultiplex, and trim out sequencing artifacts.

    Note that the tutorial uses a toy data set with single-end reads. Since you have paired-end data, you’ll want to use --type MultiplexedPairedEndBarcodeInSequence in the qiime tools import command, and qiime cutadapt demux-paired and qiime cutadapt trim-paired instead of the single-end versions of those commands used in the tutorial.

  3. Once you have demultiplexed and trimmed out all sequencing artifacts, you can proceed with denoising your data with DADA2 or Deblur (e.g. see this section of the Moving Pictures tutorial; since you have paired-end data the commands will differ slightly). We don’t have official support for denoising IonTorrent data yet, but the current recommendation from the DADA2 developer is to use --p-trim-left 15 to trim off the first 15 bases during denoising (see this forum topic for details).

Let us know how it goes!

PS: If you haven’t already, I highly recommend working through the Getting Started guide and the Moving Pictures tutorial before getting started with your own data set. Thanks!