cave updates

mdehollander · Oct 12, 2024 · e80e2c4 · e80e2c4
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commit e80e2c4
Showing 1 changed file with 8 additions and 5 deletions.
diff --git 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 CH₄ (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)
+