How to get visualization of already analysed data?

User Support
1

Hi everyone!
I'm new in the microbiome field and have very little idea about how things and novice in coding and programming.
I already have analyzed and simplified microbiome data of my sample done by another company [https://www.ezbiocloud.net/] under collaboration with my Professor's lab.
The problem lies that I don't have raw file in FASTq format and Ezbiocloud platform gives my results in excel format with alpha diversity, beta diversity, and LEfSe analysis (easy comparison between control and diseased state). Further looking up into this, Ezbiocloud gives analyzed individual samples file TSV and JSON format. I have attached a zip folder for your reference. O9414S113757.zip (17.6 KB)

Example of .tsv file:

Full taxonomy Name or group Read count Copy-number corrected read count
Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroidaceae_uc Bacteroidaceae_uc 43 25

I tried to dig more into individual samples, i get raw_xy.fasta [FASTA file] of individual phylum for 1 sample (7-8 FASTA files for 1 sample).

My only problem is that i don't have the visualization except bar plots for my data and also i need to find correlation of microbiome between my samples (control vs diseased state).

Any advise or help would be appreciated.
-Hari

1 Like
2

Hi @phrhari,

Welcome to the :qiime2: forum!

If you have a table of features, you could import that into QIIME 2 (this would be an excel sheet with taxonomy or an OTU ID or something similar as a row or column and your samples along the other axis). You could definately import your alpha and beta diversity here and then use QIIME for your downstream analysis (PCoAs, adonis or kruskal wallis testing, etc).

If you want to do that, I'm going to refer you to the Importing Data tutorial... skip down to the end.

Best,
Justine

1 Like
3

Hello Ma'am,
I tried with what you have suggested but it didn't work for me.
I'm getting:
(1/2) Missing option "--m-input-file".
(2/2) Got unexpected extra argument (O9414S113757.tsv)
Any suggestion would be appreciable.

-Hari

5

Hi @phrhari,

Could you give the commands you ran, please? Its hard to trouble shoot the error without knowing where in the process it is.

Best,
Justine

1 Like
6

Hello Ma’am,

I’m sorry for not elaborative earlier.
I used below command as have a file in .tsv format which I described in my first query:
qiime metadata tabulate
–m-input-file sample-metadata.tsv
–o-visualization tabulated-sample-metadata.qzv

And i got:
(1/2) Missing option “–m-input-file”.
(2/2) Got unexpected extra argument (O9414S113757.tsv)
I’m still not getting how to sum up individual TSV files and visualize them. As they all are already analyzed by company and results are in excel in this format:

Taxon name; Taxon rank; Taxonomy; LDA effect size; p-value p-value (FDR); Control group; Treatment 1;Treatment 2

Regards,
Hari

8

Hi @phrhari,

I think you need to format your command with line wraps:

qiime metadata tabulate \
–m-input-file sample-metadata.tsv \
–o-visualization tabulated-sample-metadata.qzv \

I dont think LefSe is a statistically appropriate analysis for this data, as its not compositional so my advice is to start from the table and run your statistics and visualization from that. You should compile it into a single file.

Best,
Justine

1 Like
9

Hi Ma'am,

That was one analysis done by other company. and I have compositional data as well in excel format. Also PCoA and alpha diversity values in excel format Apart from box plot or bar graph I cant have other analyses or visualization of my data.
I wanted to do pairwise correlation analysis.
I may sound lost but is there any other way I can use my excel data to do more analysis of microbiome data that would be very helpful to me.

Thank you again for your support

Regards
Hari

10

Hi @phrhari,

If you want to visualize your distance matrix and do statistics, you can import that. LefSe results should be disregarded, just import your table and analyze from there. Otherwise, ask the company for your raw data and start over. They should provide you with your raw sequencing data.

Best,
Justine

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