Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Occupancy modelling of sequencing data

AD Anni Djurhuus
CC Collin J. Closek
RK Ryan P. Kelly
KP Kathleen J. Pitz
RM Reiko P. Michisaki
HS Hilary A. Starks
KW Kristine R. Walz
EA Elizabeth A. Andruszkiewicz
EO Emily Olesin
KH Katherine Hubbard
EM Enrique Montes
DO Daniel Otis
FM Frank E. Muller-Karger
FC Francisco P. Chavez
AB Alexandria B. Boehm
MB Mya Breitbart
request Request a Protocol
ask Ask a question
Favorite

For each individual-locus dataset, the first step of decontamination was to determine the OTUs likely to be truly present in the dataset vs. those likely to be false-positive discoveries (e.g., artefacts of PCR or sequencing), see Supplementary Fig. 2. We used a site-occupancy model to estimate the probability of OTU occurrence51,52, using multiple PCR replicates of each environmental sample as independent draws from a common binomial distribution. We eliminated any OTU with <80% estimated probability of occurrence (a break point in the observed distribution of occupancy probabilities) from the dataset.

Copyright and License information: The Author(s) ©2020
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A