SEM1b-CAZymes

This repo reproduces the computational analysis presented in the paper "From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus." (https://www.biorxiv.org/content/early/2018/07/11/280602).

File structure

• CAZ_SEM1b.Rmd: Notebook to reproduce the analysis
• results\CAZ_SEM1b.html: Knitted version of the notebook, pictures and results are already generated
• Data\16Stimeseries_raw.txt: 16S amplicon read counts
• Data\CelluloseDegratation.txt: Cellulose utilization
• Data\ProteinConcentration.txt: Protein concentration
• Data\Sacch_table.txt: Saccharides quantification
• Data\caz_selected.txt: CAZymes annotated on the ORFs
• Data\caz_selected_ext.txt: CAZymes annotated on the gene groups
• Data\collapsed.mus: Transcript estimation for the gene groups
• Data\collapsed.uniques: Unique hits for the gene groups
• Data\not_collapsed.mus: Transcript estimation for the ORFs
• Data\not_collapsed.uniques: Unique hits for the ORFs
• Data\SpikeIn_counts: RNA spike-in counts

Notes

Please be sure to install the required R and python libraries and to have an updated version of Rstudio (>=1.2.830).