# Enquiry for lefse analysis

**URL:** <https://forum.biobakery.org/t/enquiry-for-lefse-analysis/950>\
**Category:** LEfSe\
**Created:** [August 31, 2020, 4:06pm UTC](https://forum.biobakery.org/t/enquiry-for-lefse-analysis/950 "2020-08-31T16:06:41Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [August 31, 2020, 4:06pm UTC](https://forum.biobakery.org/t/enquiry-for-lefse-analysis/950/1 "2020-08-31T16:06:41Z")

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I have come across many papers using lefse for statistical analysis of NGS data. I have followed this tutorial for reference [https://github.com/biobakery/biobakery/wiki/lefse#notes](https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_biobakery_biobakery_wiki_lefse-23notes&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=RTU5rsFiNDjZ3naB0Azw6z7ejirU5PmYxqahrIPMGEs&m=VUauMJbZma4-3raxvKmoXnkabtpmgN7L9Ix2j8oYG-Y&s=iIy9oX-6_KF2LbBzysobo-pPQ340a9gu36LX629Al1M&e=)

I want to apply lefse in my analysis too. However, I did not succeed to format my OTU data to input it in lefse for analysis. OTU frequency table was analyzed through Qiime2.

Please do kindly help.

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**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [August 31, 2020, 4:13pm UTC](https://forum.biobakery.org/t/enquiry-for-lefse-analysis/950/2 "2020-08-31T16:13:58Z")

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Hi **H. Nakibapher Jones Shangpliang** ,

Please direct to [hmp\_small\_aerobiosis.txt](https://raw.githubusercontent.com/biobakery/biobakery/master/demos/biobakery_demos/data/lefse/input/hmp_small_aerobiosis.txt) to see an example LEfSe input file. Additionally, would it be possible for you to provide your input sample/example data to look more into the issue?

Thanks,  
Sagun

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**Author:** ![Shangpliang.HNJ](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/shangpliang.hnj/32/370_2.png) [@Shangpliang.HNJ](https://forum.biobakery.org/u/Shangpliang.HNJ)\
**Post date:** [September 1, 2020, 7:13am UTC](https://forum.biobakery.org/t/enquiry-for-lefse-analysis/950/3 "2020-09-01T07:13:36Z")

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Thank you Sir for your reply.

I have gone through the [https://raw.githubusercontent.com/biobakery/biobakery/master/demos/biobakery\_demos/data/lefse/input/hmp\_small\_aerobiosis.txt](https://raw.githubusercontent.com/biobakery/biobakery/master/demos/biobakery_demos/data/lefse/input/hmp_small_aerobiosis.txt) I have also tried the analysis using the tutorial link above.  
However, the content of the sample data is different from my data. Please do kindly see my sample data sna maybe you can help. Thanking you. Have a blessed day.  
[Sample\_for\_lefse\_Shangpliang.txt](https://forum.biobakery.org/uploads/short-url/lI1mo0fFxecAh24eFk4MGQi87oS.txt) (4.1 KB)

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**Author:** ![george-weingart](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/george-weingart/32/256_2.png) [@george-weingart](https://forum.biobakery.org/u/george-weingart)\
**Post date:** [September 17, 2020, 10:14pm UTC](https://forum.biobakery.org/t/enquiry-for-lefse-analysis/950/4 "2020-09-17T22:14:37Z")

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Hello Shangpliang,

I tried to run Lefse in Galaxy using your data and it runs OK, the only issue is that id does not find any discriminant features in your data.  
Let me know if you have any further questions.  
Best regards,  
George Weingart PhD  
Huttenhower Lab

 ![Screen Shot 2020-09-17 at 3.13.14 PM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/edded1db195a7535c880b806e6e5cc477be831e6.png)