QIIME2 virtual box help

Hi,
I assume this might have been answered but considering my ignorance to QIIME and general bioinformatics skills, I would really appreciate if someone could proceed to still help me.
I have installed QIIME2 in a virtual Box, I have also linked the drive containing my data. My data is meta genomic data from Illumina and I have got all the fastq demultiplexed files in one folder for a particular Season. Example, for Season 1 i.e. S1, I have the folder with 20 fastq text files with forward and reverse for each 20.
I am clueless as to hoe to proceed with importing or working with the files in QIIME. I ran the tutorial of QIIME to test my installation. However, that is just incorporating data from tutorial. I am still struggling to get my data in terms with qiime artefact and how to proceed in virtual box.

I will be grateful for any help. I have read several tutorials but unfortunately, I am still struggling. All I have currently is qiime installed in virtual box an my 16s meta genomic data for different seasons with each season folder having 20demultiplexed forward and reverse fastq sequences.

Kind regards

Hello Ankita,

I’m glad you got the VM installed and were able to run the tutorial. Let’s see if I can get you started with your data.

It sounds like you could use the fastq-manifast-formats to import your data. Once you have imported it, you can follow the steps in the tutorials.

Let me know if the fastq-manifast format works well for you. Feel free to post any questions or errors you find along the way.

Colin

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Hi Colin,

Thanks very much for trying to help me. So, if I understand correctly, after I make the manifest file. How should I proceed in my virtual box? I will make the manifest file now and say that I have the manifest.csv file.
I am sorry, I know I sound like a lame person but any help in first hiccups would be great for me as of now.

Kind regards
Ankita

Hello Ankita,

No worries! I know it hard to get started without a tutorial to guide you.

The good news is that some of the documentation includes good examples. If we go back to the fastq-manifest-examples, we can scroll to the bottom and find the two examples of Importing Data. You mentioned you have paired end reads, so you this example is probably best:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path pe-64-manifest \
  --output-path paired-end-demux.qza \
  --source-format PairedEndFastqManifestPhred64

But wait! How do you know to use PairedEndFastqManifestPhred64 or PairedEndFastqManifestPhred33? You just try it both ways and see if it works better.

Trial and error works great for stuff like this. Let me know what you try next!

Colin

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Hi Colin,

Thank you for understanding my situation. Unfortunately, I don’t have access to my system this weekend to try further. However, I did try to run the Cassava import method which seems to have wrapped my 22 sequences into a .qza file. I understand as long as the sequences for analysis are wrapped in the artefact file, we are good to experiment with utilising QIIME functionality. Is there any chance that I need to still import it using the above mentioned method?

I would definitely be touching base on Monday again with my next hurdles.

Thanks you and Have a good weekend

Kind regards
Ankita

Hello Ankita,

If the Cassava import let’s you see all the samples you expect when you make your graphs, I would say it worked!

Demultiplexing is tricky because there are many, many ways of doing it, so it’s hard to choose. But as long as you see all your samples, you are good to go.

Have a good weekend. Feel free to post more questions or open a new thread if you have more questions!

Colin

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