Tutorial - Data imports

Continuing the discussion from Greetings!:

Kindly advice me on how to import my sequencing read into qiime2 from my machine (shared folder). The tutorial explained data import by downloading the barcodes and the fastaq files from the internet, how do I import to qiime2 when using my personal computer i.e. my sequence reads are already downloaded on my computer, how do I import the data into qiime in order to start the preprocessing of the sequence reads and others?ntinuing the discussion from Greetings!:

Hi @bettya and welcome to the forum :wave:

It’s not clear to me how your situation differs from the workflow in the tutorials. If you could please elaborate on the questions below, that would be very helpful.

  • what did you try?
  • what were the expected results?
  • what were the actual results and how did those differ from your expectations?

Hi Andrew
Good to hear from you.
I am a beginner, learning qiime to analyze microbiology data on my own.
My qiime2 language and terms is not yet sound so I sometimes express terms wrongly.
I received my 16S reads from Mr DNA and I downloaded it from their cloud storage to my desktop folder, but I need to import the data to qiime in order to begin the processing of the data, how do I get to create a path to the reads in my computer shared folder (desktop)?
I found a software on Mr DNA site that helps to create path to the reads in order to begin import into qiime.
I want to try it today, but I will get back to you if I am able to do it.
Thanks.

Betty
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Hi Adrew
What I want to know is how to transfer my already downloaded reads into qiime (I downloaded my data from an online facility). I am using virtual box for qiime2 and I am also a beginner. I tried all the tutorials and things seem fine until I have to use my own data and I found that I cannot use the import script as described in the tutorial. I read somewhere that I have to transfer the data into qiime but no script available for that. Kindly help me!
I am working on 16S and ITS data for my PhD and I need to study abundance and diversity studies on my samples.
Thank you.

Hi @bettya,

What form are your data in? Are your data already demultiplexed, i.e. you have separate sequence files for each sample? Or are your data in multiplexed form, that is you need to perform the demultiplexing (separating your data out on a per-sample basis) yourself.

Perhaps provide us some examples of the file names and what you’ve tried thus far from the various Importing approaches?

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Hi SoilRotifer
I haven’t tried any importing scripts. The reason is very simple:
Importing scripts download data online but I have my data on my computer not online.
My data has already been demultiplexed by software provided by the sequencing facility, all the barcodes and the primers were also removed from the metadata file by the software. I was left with a qiime folder that has the demux file and a validated metadata file. All the files are in correct format name.
What I need to know is how to move or transfer the file from my computer folder into qiime2 and do the denoising or dada2 step.

Okay, so you have a folder, on your local computer, full of sequence files already separated out by sample. Or do you have one single sequence file? Is it a QZA file? ZIP file? Something else?

Assuming you have a folder full of separate sequence files, it sounds like you have everything you need to import your data. You should be able to import the data following Manifest approach. Alternatively, you might also be able to import via CASAVA approach, assuming your file names fit that schema (see the CASAVA description in the link). I prefer to use the manifest approach myself.

If this is not what you have, then I am not sure what you have. As I asked earlier, can you provide some examples of the actual file names of the files you have?

-Mike

Can you elaborate on this? It sounds to me like you might have tried something that didn’t work. But you also said,

So I’m a bit confused about how you have determined that you can’t import your data.

I’m also confused about these two points because, while the tutorial data is online, you have to download that data onto your computer before running the import step. When you run the importing step, the data is on your computer, not online. The fact that the data is on your computer and not online does not introduce any additional steps whatsoever. You just need to provide qiime tools import with the path to that data on your computer.

Can you please clarify what you mean by “importing scripts.” I’m wondering if you are referring to something other than the qiime tools import command. qiime tools import does not download date from the internet.

I would highly recommend following the links that @SoilRotifer has provided above. I think taking the time to read through them will help clarify some things. :smiley:

Sorry for the confusion. I hope we can help you sort this out! :qiime2:

P.S. Sorry for leaving you hanging for so long. Thanks, @SoilRotifer, for coming to the rescue! :pray:

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Hi SoilRotifer

Thank you for your help.
I have the following files on my computer:
barcodes fastq.gz
forward fastq.gz
reverse fastq.gz
All these are in a folder called emp-paired-end-sequences
Then another folder:
sample-metadata.tsv
I have these files in a folder on my desktop which is the shared folder with qiime2 that I have installed on my computer.
I am going through the emp tutorial now.
Am I on the right path?

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Hi @bettya,

I think we are getting closer,

This is perfect! If these are indeed the files you’ve obtained from your sequencing provider, then they are helping you get set up to import via EMP Protocol, as you correctly surmised. So, you should be able to import the sequences contained within the emp-paired-end-sequences folder using the commands outlined there.

-Cheer!
-Mike

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