Qiime 2 for Ion Torrent PGM 16S rRNA

[Harry (Harry Batsang)]

My data is 16S rRNA seq using Ion Torrent PGM.

The length of ideal seqs should be 300~400, I need to delete seqs that are shorter than 300. In mothur, it is very simple to use a command minlength=300, I am wondering the command for Qiime 2.

I did not find command on the official tutorials, The reason I am posting here is that Qiime 2 always gives me errors…

Thanks a lot

[ebolyen (Evan Bolyen)]

Hey @Harry!

@Harry

The length of ideal seqs should be 300~400, I need to delete seqs that are shorter than 300. In mothur, it is very simple to use a command minlength=300, I am wondering the command for Qiime 2.

If you were to use dada2 for your processing, the equivalent parameter would be trunc-len.

Also based on this note it looks like you should set trim-left to at least 15 for Ion Torrent data.

Let me know if you need more details!

P.S. Out of curiosity, what format is the output in from an Ion Torrent sequencer? Do our current import commands work, or is this a pain-point?