ONT_pilot_w_GDB_samples.md

@@ -598,7 +598,15 @@ sourmash plot ont_hybrid_bins_sourmash_comp --labels --pdf
 ```
 
 ##### dREP #####
-# checking to see if the bins are the same
+- Binning the metaspades_hybrid assembly was a `conundrum`
+- Binners require a `bam` file (typically) to estimate coverage
+- So, the question arose which bam file should/could we use? 
+- We had the following options to choose from: bwa_sr_metaspades_hybrid, bwa_lr_metaspades_hybrid, bwa_merged_metaspades_hybrid, mmi_sr_metaspades_hybrid, mmi_lr_metaspades_hybrid, and mmi_merged_metaspades_hybrid
+- Here above, sr==short-reads mapped to assembly, lr==long-reads, and merged==merging of sr- and lr- bam files
+- If you haven't caught on to how we do things around here - we do them all 
+- This is the part of the story, I like to call "BinCHECK" using [drep](https://github.com/MrOlm/drep)
+```
+# checking to see if the bins reconstructed from different 'bam' files are similar
 cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB
 mkdir bins
 cp /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/results/Binning/checkm_output/sample_list bins/.
@@ -644,6 +652,19 @@ cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/bins
 dRep compare drep_output -g ./*.fa
 ```
 
+##### VizBin #####
+- The binners did great for the sr- and hybrid assemblies, however, fared poorly with the lr- (flye) assembly
+- A sign of a good researcher is that they never trust their own data, and validate it twelve-ways-to-Sunday
+- Not saying that I'm good, but I like to validate, for lack-of-a-better-word in my vocabulary and at my discretion, the "heck" out of something
+- And since "seeing is believing", I took the assemblies to our very own CCL's [VizBin](http://claczny.github.io/VizBin/) implemented via [BusyBee](https://ccb-microbe.cs.uni-saarland.de/busybee/)
+```
+# Running flye assemblies on the BusyBee web server
+# Downloaded the "methylation-aware" flye assembly to the Desktop
+# And uploaded it to the BusyBee server
+# Changed the minimum contig length to 1500
+# Run ID: b9d043cf-9a55-4ba8-9d1b-2bef4861cd61
+```
+
 ##### QUAST #####
 - Testing assembly stats using quast
 ```