My group has been using the Ion 16s metagenomics kit from Ion Torrent. This kit has 6 unpublished primers targeting regions: v2, v3, v4, v67, v8 and v9. I have a way to separate the reads out into their targeted regions and am left with a fasta file for each region.
Can qiime 2 be used at the fasta file step and can anyone provide any guidance for this?
Does qiime2 have any guidelines with using Ion Torrent sequencing data?
Yes. It sounds like you have demultiplexed sequences but I am not sure of the exact format (you will need to provide more details) but if you can get these into a format similar to qiime1 demultiplexed sequences, you can use the following command to import:
qiime tools import
Not yet — we do not have much experience with this format and have only had a few users working with this format (which is to say that we are very interested in learning more to support this format ).
There have been a few other posts about ion torrent data on the forum (e.g., here). If you do run into specific problems with importing, I would recommend first trawling the forum to see what other users have recommended in the past.
I hope that helps!
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