# the way features are named affect the final results of lefse

**URL:** <https://help.galaxyproject.org/t/the-way-features-are-named-affect-the-final-results-of-lefse/8338>\
**Category:** usegalaxy.org support\
**Tags:** text-manipulation, troubleshooting, lefse\
**Created:** [July 20, 2022, 4:52am UTC](https://help.galaxyproject.org/t/the-way-features-are-named-affect-the-final-results-of-lefse/8338 "2022-07-20T04:52:07Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![hlsw2001](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hlsw2001/32/3495_2.png) [@hlsw2001](https://help.galaxyproject.org/u/hlsw2001)\
**Post date:** [July 20, 2022, 4:52am UTC](https://help.galaxyproject.org/t/the-way-features-are-named-affect-the-final-results-of-lefse/8338/1 "2022-07-20T04:52:07Z")

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Hey, I encountered an issue: I was working on [Galaxy](http://huttenhower.sph.harvard.edu/galaxy/) and trying to run lefse but the output files were different when I changed the way microorganisms are named.

Here is everything that I know:

The dataset is green, the job did not fail.  
The lef\_usual.txt is a input file whose first column contained many names of microorganisms, and these names had some special characters like “()”, “-” and “'”, like “Clostridium\_sp.\_DL-VIII”.  
The lef\_usual\_result.svg is the output file. There are 5 biomarkers for “meNorChild”.

Then, I replaced all the names of microorganisms in the first column in lef\_usual.txt with another way of naming, such as s1, s2 and s3. The new input file was named lef\_number.txt.  
The lef\_number\_result.svg is the new output file. There are 11 biomarkers for “meNorChild”.

The relevant parameters of the two tasks are the same, only the naming method of the first column of the input file has changed.  
So, why does just changing the way microorganisms are named affect the final results? What format of naming will give the most correct results?  
The process screenshots, input files and output files have been uploaded.

 ![lef_number](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/91fa9fda29893aa7cab89bad0edb31f24e1f4597.png)  
 ![lef_number_result](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/e/eb92bc975a6dd198107d654f68b3d1df45cc3b32.png)  
 ![lef_usual](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/cdca97ad08002bf2849140e109dbc7455976a939.png)  
 ![lef_usual_result](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/7724835daa1efcf7ceba50a66452195b6225b88b.png)  
 ![process](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/f/f0353216d18ea73995870df00b06d3e226f65b5a.jpeg)

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [July 21, 2022, 5:31pm UTC](https://help.galaxyproject.org/t/the-way-features-are-named-affect-the-final-results-of-lefse/8338/2 "2022-07-21T17:31:23Z")

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Cross-posted here: [the way microorganisms are named affect the final results of lefse](https://help.galaxyproject.org/t/the-way-microorganisms-are-named-affect-the-final-results-of-lefse/8337)

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [July 21, 2022, 5:31pm UTC](https://help.galaxyproject.org/t/the-way-features-are-named-affect-the-final-results-of-lefse/8338/3 "2022-07-21T17:31:34Z")

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