Questions about Dokdo and LEfSe

Other Bioinformatics Tools
1

Hi @sbslee Thanks for your Dokdo tutorial, I found LEfSe easy to use!
I have a few questions below.

  1. What do the parameters '-c 1', '-u 2', '-o 1000000' signify in the 'lefse-format_input' code? Is it necessary to adjust these numbers based on my data?

$ lefse-format_input.py
output/Useful-Information/input_table.tsv
output/Useful-Information/formatted_table.in
-c 1
-u 2
-o 1000000
--output_table output/Useful-Information/formatted_table.tsv

  1. When I obtain the 'output.pdf,' there are instances where images are cropped. I'm wondering if modifying the Python file is necessary or if there's an alternative solution for this issue

Example cropped image (part of the image)
image

  1. I would like to set the center of the x-axis to 0. What steps should I take to achieve this?
    image
    image1390×271 12.9 KB

Thank you
Best wishes

2

Hello @minjoy,

I'm not sure if @.sbslee is offering support of Dokdo anymore, so I've split your question into a new threads to other folks can see it.

I'm not sure what those settings do either, through I did find this part of the docs, which may be helpful? dokdo_cli: prepare-lefse

3

Hi @minjoy,

The lefse-format_input.py simply prepares the file so that you can import into LEfSe. Which I assume you are using the online Galaxy version? If so, you need to adjust the figure settings on the website, using the options there.

-Mike

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