Holtz Lab: Analysis of Mother-Twin Infant Virome & Bacterial Microbiome

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Bacterial Microbiome Analysis

Analysis consists of six scripts:

QC & Pre-processing

1. TwinMom16S_Quality_ErrorRate_Checking.Rmd
2. TwinMom16S_dada2.R

Data Cleaning

3. TwinMom16S_Pre-processing.Rmd

Analyses

4. TwinMom16S_Analysis (main bacterial analysis)
5. TwinMom16S_Shared_RelAbd_Plots.Rmd (shared bacterial taxa analyses)
6. TwinMom16S_Supplemental_Analysis.Rmd (supplemental bacterial analyses)

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Virome

Pre-processing

Raw sequencing data was processed through VirusSeeker Virome v0.063 (https://wupathlabs.wustl.edu/virusseeker/). Phage reads and corresponding blastX files were used to generate .RMA files for each sample in MEGAN6 Community Edition v6.10.5 using the script run_blast2rma.sh. RMA files were used to generate the Compare file using absolute counts and ignoring unclassified reads. A BIOM1 file was then created using the following steps in MEGAN6:

1. Opened compare file
2. Selected virus node
3. Uncollapsed subtree below virus node
4. Selected subtree
5. File > Export > BIOM1 Format... > (export taxa at official ranks only?) > No
6. Saved .biom file
7. .biom file was used to generate a phyloseq object (physeqPhageSelectTaxa.RDS - see TwinMomPhage_Pre-processing.Rmd) that was utilized in the remainder of analyses.