Qiime2 with IonTorrent data

[Claudio (Hidalgo)]

Hey guys, a question before starting my analysis...I have IonTorrent .fastq files that the guy from the sequencing provider gave me. I have 40 files for the 40 individuals of the analysis, one file for each with single-end reads. I do not have any text file with barcodes.
Checking the import data tutorial I think the EMP protocol or the Casava will not work. Is this right? The unique alternative is to create the .fastq manifest?

Thanks

[Nicholas_Bokulich]

@Claudio

Checking the import data tutorial I think the EMP protocol or the Casava will not work. Is this right? The unique alternative is to create the .fastq manifest?

Correct. EMP is a multiplexed format. Casava 1.8 is specific to Illumina files in that format. Manifest is the catch-all format for demultiplexed files.

There are various other posts on this forum about analyzing ion torrent data — you may want to check those out to see how other users have dealt with their data for importing and post-importing processing.

I hope that helps!

[Claudio (Hidalgo)]

Thanks Nicholas. I was able to create the manifest-file and import the data!! Great achievement for the first day as I am not a bioinformatic at all.

I will keep bodering with more questions for sure

Thanks