How to do multiplex of Ion torrent sequences

User Support
7

Good morning Khemlal,

That's a very helpful diagram! I'm not very familiar with the Ion Torrent PFM platform, but here is what I would try first.

  1. Build your manifest file and save it as se-33-manifest.csv. Maybe like this:
sample-id,absolute-filepath,direction
# Lines starting with '#' are ignored and can be used to create
# "comments" or even "comment out" entries
sample-8,$PWD/some/filepath/V3-341F8-.fastq,forward
sample-9,$PWD/some/filepath/V3-341F9-.fastq,forward
sample-10,$PWD/some/filepath/V3-341F10-.fastq,forward
...
more samples
...
sample-46,$PWD/some/filepath/V3-341F46-.fastq,forward
  1. Then import your reads:
qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-path se-33-manifest.csv \
  --output-path single-end-demux.qza \
  --source-format SingleEndFastqManifestPhred33

Let me know how well that process works. One key question for me is how the Ion Torrent goes about 'merging' the forward and reverse reads. This could change our demultiplexing strategy.

Colin

2 Likes