Qiime2 ECAM tutorial data

General Discussion
1

Hello,

Can anyone please let me know another way of acquiring the data used in the qiime2 ECAM tutorial?
The Qiita website is currently under maintenance; therefore, I can't access the sequence files.

Thank you in advance!

2

Hi @broadeavintes and welcome to the forum!

I assume that you are following this tutorial? https://curr-protoc-bioinformatics.qiime2.org/

You could get the data from SRA, accession # PRJEB14529

There is a QIIME 2 plugin, q2-fondue, that will allow downloading data from SRA using the accession ID.

However:

  1. The tutorial above uses a smaller subset of the data, so it might not work with the full dataset (or at the very least some steps might be different and it will take longer to compute).
  2. Qiita is where the data were originally uploaded. The data on SRA were automatically ported over via way of EBI, so some things may have changed (e.g., it looks like only single-end reads were ported over).

So you could definitely start with SRA and skip Qiita — but some things will be different from in the tutorial. To run things exactly as they are in the tutorial ("out of the box"), you might be better off waiting for the Qiita maintenance to finish.

1 Like
3

Thank you for the quick reply! Will have that in mind.