Importing Ion Torrent data

[osaama.shehzad]

I have three samples sequenced (16srRNA V3 regions) using Ion 16S Metagenomics Kit and I want to perform alpha & beta diversity analysis. The sample files are single-end, demultiplexed but how do I import them into QIIME? I tried casava single-end method but it gives an error apparently because naming is not correct. Also, how to create "fastq.qz" file? Please guide me on how to successfully import my samples into QIIME. Step by step approach is highly appreciated because I am a newbie to both bioinformatics and QIIME

[osaama.shehzad]

Hi @jairideout !

Can you please guide me on how to import my data after I have successfully converted it to FASTQ? My sequence data is already demultiplexed by the IonTorrent sequencer. It consists of 3 samples (one FASTQ file for each). Here is the screenshot:

003, 004, 005 are the barcode numbers in the names of the files and they have been trimmed already so these are all demultiplexed FASTQ data files.

The end goal of my project is following:

1. perform alpha AND beta diversity analysis
2. construct a phylogenetic tree

But i can't do that since I am having a lot of trouble importing the data. Your help will be highly appreciated!

[ebolyen (Evan Bolyen)]

Note for other readers: I’ve merged this reply into the topic (instead of rejecting it as a duplicate) as it contains a couple more pieces of information.

[thermokarst]

Hi @osaama.shehzad! Sorry to hear you’re having a hard time - lets fix that!

Your sequences are a perfect match for our fastq manifest format! This will let you import your reads (it will also gzip them for you, since you were asking about that in your first post). Please read that document and give it a shot. There are also many forum posts here about importing using this manifest format, so if you get stuck please check those out!

Keep us posted!

[osaama.shehzad]

Hi @thermokarst! Thank you so much! I have successfully imported the data and I am performing DADA noise blur as I write this reply. Once, I am done with diversity analysis and phylogeny, I will update you. If everything goes as planned, I would love to share a flowchart which can also guide future IonTorrent users on how to play around with QIIME.