diff --git a/docs/data-processing/cave-expedition.md b/docs/data-processing/cave-expedition.md index f4b5f7c..20124ad 100644 --- a/docs/data-processing/cave-expedition.md +++ b/docs/data-processing/cave-expedition.md @@ -5,10 +5,12 @@ ![Cave Microbiome Sampling](../assets/cave1-1.png) (a) General overview of the cave. (b) Detailed images of the cave biofilms. The dashed line in panel a marks the stable gaseous chemocline between the volcanic gases (below the chemocline) and atmospheric air (above the chemocline). (c) A closer look on the biofilm where mark 7 shows the bare cave wall after biofilm sampling. +[Watch the video of bubbles drifting along the invisible stream of greenhouse gases (for fun).](https://www.gesslab.org/projects?wix-vod-video-id=a7aaef92d15549e6a5630d18e73484b7&wix-vod-comp-id=comp-jd73rsf5) + Data are precomputed and store at folder /data/precomputed/cave_data containing: -- co-assembly (3 samples; 2 from biofilm and 1 from the laboratory) -- Depth table -- Binning results + - co-assembly (3 samples; 2 from biofilm and 1 from the laboratory) + - Depth table + - Binning results !!! question "Exercise" - Analyze the microbial bins to identify which organism is utilizing CHâ‚„ (methane) for growth. What is the taxonomic classification of this organism? Investigate the presence of relevant gene clusters responsible for methane metabolism. @@ -21,8 +23,9 @@ Data are precomputed and store at folder /data/precomputed/cave_data containing: - Assign taxonomies to the bins with GTDB-Tk for precise classification. - Predict open reading frames (ORFs) using Prodigal and functionally annotate the bins through EggNOG for a deeper understanding of their metabolic capabilities. -??? done "Tip 2: which functions to look for" +??? done "Tip 2" - Investigate the gene annotation for methane monooxygenase and reductive TCA cycle and analyze the surrounding genomic regions to identify nearby genes and their associated protein functions. + - Calculate the abundance of each bin by integrating the depth table with the binning results (use python/R). -[Watch the video](https://www.gesslab.org/projects?wix-vod-video-id=a7aaef92d15549e6a5630d18e73484b7&wix-vod-comp-id=comp-jd73rsf5) +