The gut microbiome of wild American marten in the Upper Peninsula of Michigan
Authors/Creators
- 1. Northern Michigan University, Wildlife Ecology and Conservation Science Lab, Department of Biology, Michigan
- 2. North Carolina State University, Department of Applied Ecology, North Carolina
- 3. University of Washington, School of Environment and Forest Sciences, Washington
- 4. Northern Michigan University, Wildlife Ecology and Conservation Science Lab, Department of Earth, Environmental, and Geographical Sciences, Michigan
- 5. Virginia Polytechnic Institute and State University, Department of Biological Sciences, Virginia
- 6. Michigan Department of Natural Resources, Michigan
Description
Directory Information for The gut microbiome of wild American marten in the Upper Peninsula of Michigan
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"R Code" contains:
--- "marten_phyobj.rds" is the phyloseq object that can be directly imported for statistical analysis if the user prefers not to go entire QIIME2 pipeline. The phyloseq object was created from QIIME2 artifacts from the "QIIMEpipe.html" pipeline: the cleaned rooted tree, the cleaned taxonomy table and the cleaned ASV table. This requires the command "readRDS()" to import. The "load()" command will not work.
--- "Stat.Rmd" Markdown file for "Stat.html"
--- "Stat.html" knitted statistical analysis file to view the studies outputs quickly
--- "Stat.R" R code if user prefers over Rmarkdown
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"QIIME" contains:
--- "martendemux.qza" demultiplexed QIIME2 artifact
--- "martendemux.qzv" visualization output of demultiplexed sequence that can be viewed at qiimeview.org
--- "MartenMeta.tsv" metadata file for QIIME2 pipeline and statistical analysis
--- "QIIMepipe.html" code for bioinformatic pipeline for downstream analysis
- "Sequences" folder:
--- "R1_demultiplxed_pairedend_marten.fastq.gz" forward reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2.
--- "R2_demultiplxed_pairedend_marten.fastq.gz" reverse reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2.