Import Ion .fastq file

[shwane (shwan)]

Hello everyone,

I have fastq file (Ion torrent PGM platform - 400bp) that are multiplexed. I am struggling in importing it to qiime2.

How can I do it? please

Thanks

[Nicholas_Bokulich]

Hi @shwane,
Many other forum users have asked this same question — have you had a chance to review those posts and try out the solutions described there?

In short, I think you probably want one of the manifest formats

Please look over those posts, try those solutions, and let us know specifically what error you are running into so we can help out.

I hope that helps!

[shwane (shwan)]

Hi @Nicholas_Bokulich

thank you very much for answering my questions. My problem exactly like @ Ion torrent sequences analysis . I have one fastq file (24 samples) and I don’t have a separate barcode fastq.gz file but I can create metadata contain barcode for each sample.

[Nicholas_Bokulich]

@shwane

I have one fastq file (24 samples) and I don’t have a separate barcode fastq.gz file

You could follow this tutorial to see if that works for you.

@shwane

but I can create metadata contain barcode for each sample.

So that's another option — create a separate barcodes file and import as EMP format.

I hope that helps!

[bahti_yil (Bahtiyar Yilmaz)]

Hey Shwane,

Did you manage to run ion torrent fastq file in QIIME 2. Would it be possible to share with us how you did at least initial part where you import the data?

Thanks a lot.