Input file for STAMP

[kkalya...@gmail.com]

Hello everyone.

I need help in preparing the profile file for STAMP. I need to prepare the .txt file. I encountered several errors. I am attaching the sample file. Kindly help.

 I would like to know if the blank taxa have to be written as unclassified.

It would be really nice if I could get access to a demo input file that has worked.

Regards

[Andre Comeau]

Yes, all lines/columns/cells have to be completely filled in order for the file to work. You also have an error that your sample1 number is missing for the first line/taxon.

What are you using to analyze your sequences? Our SOPs/QIIME2 should be generating a feature table that is compatible with STAMP, as long as you follow the small extra step of running the scripts in the STAMP directions: https://github.com/LangilleLab/microbiome_helper/wiki/STAMP-preparation

A file for STAMP is going to look something like this:

Level_1	Level_2	Level_3	Level_4	Level_5	Level_6	Level_7	A20723	A20901	A30723	A40723	B10901	B20901	C10901	C20901
d__Bacteria	p__Cyanobacteria	c__Cyanobacteriia	o__Chloroplast	f__Chloroplast	g__Chloroplast	s__Melosira_varians	7572	5	906	1048	0	0	0	0
d__Bacteria	p__Cyanobacteria	c__Cyanobacteriia	o__Chloroplast	f__Chloroplast	g__Chloroplast	Unclassified	0	0	0	0	50	23	5045	1122
d__Bacteria	p__Cyanobacteria	c__Cyanobacteriia	o__Cyanobacteriales	f__Phormidiaceae	g__Tychonema_CCAP_1459-11B	Unclassified	0	596	0	0	0	0	0	0
d__Bacteria	p__Cyanobacteria	c__Cyanobacteriia	o__Chloroplast	f__Chloroplast	g__Chloroplast	s__Spirogyra_pratensis	0	0	0	0	255	156	0	0

Alternatively, the "Level_1" labels, etc. should be able to be exchanged for your "real" labels of Domain, Phylum, etc.

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of kkalya...@gmail.com <kkalya...@gmail.com>
Sent: Friday, June 17, 2022 11:10 AM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] Input file for STAMP

 

CAUTION: The Sender of this email is not from within Dalhousie.

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[kalyani karandikar]

Thank you for your prompt reply.I will make tge required changes and update my progress.

Regards

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[kalyani karandikar]

Hello Andre,

 I modified the file as suggested by you. Now I am getting an error- Data does not form a strict hierarchy. Child s__ has multiple parents eg(g__Enterococcus, g__ streptococcus).

Kindly advise on how to resolve this issue.

Thanks in advance

Regards

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Kalyani Karandikar

Ph.D. Student

National Institute For Research In Reproductive Health

Parel, Mumbai

[Andre Comeau]

Yes, you cannot have the same named cells at Level7 (or any level) for different genera at Level6 (ie: all strings down to the final level must be completely unique).

If you have species "s__" (which is nothing/unclassified) in more than one genus above in L6, then it thinks "s__" is polyphyletic and it can't handle it.

In the example in your email: you would need to have "s__Unclassified_Enterococcus" and "s__Unclassified_Streptococcus" at L7 for it to work.

In the example in the table below: you would need to have "s__Unclassified_Chloroplast" and "s__Unclassified_Tychonema" at L7 for it to work.

This is why I mentioned the STAMP preparation scripts below in my previous email as there is one there (fix_spf.py) that looks for these hierarchy problems and tries to fix them (it usually finds most of them, the rest can be fixed manually as above).

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of kalyani karandikar <kkalya...@gmail.com>
Sent: Saturday, June 18, 2022 2:51 AM
To: microbio...@googlegroups.com <microbio...@googlegroups.com>
Subject: Re: [microbiome-helper] Input file for STAMP

 

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