Ion Torrent data denoise with dada2

[thermokarst]

Hi @MMC_northS!

@MMC_northS

i used that one because I do not have paired-end sequences so I assume that they do not pre-joined (nothing to join). In this case I can use dada2 for single-end option? or it is most adequate use deblur denoise?

If they are single end, but pre-joined from the ion torrent processing step, you will need to import them as SampleData[JoinedSequencesWithQuality], otherwise you can import them as SampleData[SequencesWithQuality] --- we have no way of know about what kind of data your reads represent, so this is something you will need to take care of understanding prior to importing.

@MMC_northS

Other question that I have is if it is good use deblur or I can use vsearch with open-reference-otu-picking directly after filtering by quality. Because I do not want trim my sequences and I can filter by number of reads or abundance later.

You are good to go either direction. Just to clarify though, there is no requirement that you trim your reads, per se - its just that deblur expects your reads to be a consistent length. Depending on the sequencing technology used, you can get this without any trimming.

Hope that helps!