low rel. abundance results

[S. Kose]

Hi all,

I hope you're well. 

I have gone through the meta pipeline (SOPv2) on the wiki site and have some pathway results I want to double check. The rel. abundance seems quite low. Is this to be expected? 

Please see below example: 

Thanks,

[Andre Comeau]

Yes, depending on your sample origins and community composition, you can have quite small numbers of RPKMs (leading to small relative abundances) for any one pathway which may not contain many genes in it, hence you might not get many hits. For example, here below are my data (in RPKMs) for the highest coverage pathway and then your same PWY-6470...and at the end is the sum for each:

pathway	N1	N2	N3	P12OR1	P12OR2	P18O	P3O	P9O	P13O	P5O	P11O	P17O	P1O	P7O	P14O	P4O	P10O	P16O	P2O	P8O	P15O	SUM
pathway	Natural	Natural	Natural	Control	Control	Control	COHort	COHort	COHort	COHort+LO-ST	COHort+LO-ST	COHort+LO-ST	COVG	COVG	COVG	COVG+LO-ST	COVG+LO-ST	COVG+LO-ST	LO-ST	LO-ST	LO-ST
PWY-7208	647.1506	609.2775	680.4121	738.2336	666.4481	626.2827	690.3316	718.4786	886.3653	745.3282	714.3409	709.0678	679.3671	691.8827	727.216	705.1641	596.689	786.0171	726.471	843.9588	756.7719	14945.3
PWY-6470	0	0	0	0	0	3.1495	13.7024	0	0	5.742	0	8.6929	0	0	0	0	0	0	0	0	0	31.3

...so you're getting certainly more hits to that pathway than I was in my soil metagenomes.

	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
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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of S. Kose <sureyy...@gmail.com>
Sent: October 8, 2024 7:01 AM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] low rel. abundance results

 

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