Why are my beta diversity results different from the tutorial?

Hi Dr. Debelius @jwdebelius

You answered my queries-thanks a lot! Also, putting multiple columns on the metadata for both numeric and categorical is a clever hack-thanks!
There's one other thing that's been bugging me ever since the day I started work on QIIME2, if you would please help me out here: It's about writing the scripts in the command prompt:

So, here's how I write my commands (example command):

PS: You will notice how I give a space after the end of a command, followed by a \ - - (spaces added for visual clarity)
output: pairwise-distances-2.qzv (left box plot)

If I copy-and-paste the same command from the tutorial, here's how it looks in the command prompt:

output: pairwise-distances-qiime.qzv (right box plot)

Comparing both outputs, they are different:

Why is this so? Am I:
a. writing the scripts in a wrong format (although they seem to work fine and output the artefacts/visualizations!)
b. It is statistical error?

I am using Qiime2 Ver 2019.10

Thank you for your time,
Best,
Anirban

Hi @anirban.mcgill,

What you’re seeing is, likely, in part an artifact of rarefaction. Rarefaction is a random process and so, depending on how you re-sample the data, you may see slightly variations in your results. Both are correct answers.

Best,
Justine

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Hi Dr. Debelius,

Thanks for your quick reply!

So, the way I am writing the scripts is correct even though it is not how tutorial scripts seem to visually appear in the command prompt?

Am I correct in saying that if my scripts were written in an incorrect format, QIIME2 would give an error instead of a visualization?

Best,
Anirban

Hi @anirban.mcgill,

Commands can be written horizontally or with line breaks ('\) and the command line reads them the same way. Most people who do a lot of programming tend to do line wrapping because it makes it easier to read/check steps, but you can totally write them on a single line with no breaks. And, yes, there’s a fairly robust error system that lets you know if the command is entered incorrectly. It will even prompt you to fix the spelling, for example, if that’s an issue.

Best,
Justine

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Ah, I get it. That explains things. Just a last add-on (I realize it’s very late in Sweden, I am very apologetic), this is what you refer as ‘on a single line with no breaks’:

qiime gneiss balance-taxonomy '\–i-table my-table.qza '\–i-tree my-tree.qza
(please ignore all the characters. They are to highlight the formatting.
There is a space between taxonomy and the backslash character without any ')

Thanks a ton, I am really grateful for your quick replies,
Best,
Anirban

Hi @anirban.mcgill,

The default way to write a single line command is something like this, where the arguments are seperated by spaces and there are no \ characters included.

qiime diversity pcoa --i-distance-matrix dm.qza --o-pcoa pcoa.qza

If you want to do line-wrapping so each argument is on its own line - whcih can make it easier to read - you can use the \ character in bash to indicate a continuation:

qiime diversity pcoa \
 --i-distance-matrix dm.qza \
 --o-pcoa pcoa.qza

Best,
Justine

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