Sinuses 2023

Exploratory bioinformatic and data analysis for rhinosinusitis microbiome project. 16S sequencing to metagenomic sequencing.

Log

metagenomic sequencing discarded - contamination with host reads is too high (>95%)
running mock communities for 16S V3-V4 (341F-805R)
- relative abundances are off
- notebook: notebooks/mock-community-bacteria.ipynb
- results barplot: visualizations/mock/gg2-barplot.qzv
running mock communities for ITS1:
- the UNITE database is too big - should be run in bash with TMPDIR reassigned and enough space
- the only detected species is C. neoformans
- notebook: notebooks/mock-community-fungi.ipynb
- resulting barplot: visualizations/mock/taxonomy-barplot-fungi.qzv
results can be downloaded to any computer and opened with QIIME2 View

many reads (> 95%) are mapped to host
- double-checked code, currently copies Qiita workflow
trying alternative refrence NCBI GRCh38 from Illumina instead of one downloaded straight from NCBI.
the situation was not resolved, see notebook
most samples contain <1% of non-human reads