# Hack MD of Hack MDs [8/18/20-8/20/20 - CRC Scripts for genome assembly, including Fastqc, Trimmomatic, Velvet, and Glimmer](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/H1NojYYMw) [8/25/20 - Julia Assembly](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/H1AOChfmw) [String Alignment](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/rkbMol3Xw) [Review 09-03-20](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/ryf71iAQP) [9/8/20 - Trimming and SNPs](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/SJg1HVSNw) [9/15/20 - Variant Calling in Julia ](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/HkT3OdCND) [9/17/20 -Visualization of VCF in Julia using Viva](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/ryX9HfZBP) [9/22/20 - GeneticVariants.jl](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/BJtWoiDHD) [9/29/20 - RNASeq in Salmon/R](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/SkwWM4WHv) [10/06/20 - RNASeq in Julia](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/HyPHk7c8D) [10/13/20](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/r14UjLmvv) [10/15/20](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/B1WgpgUPw) [10/20/20 - Pop Gen Day 1](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/HyFpN93PD) [10/27/20 - Fitness Landscapes](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/H13yy0S_v) [11/3/20 - Converting R to julia - pdClust example](https://hackmd.io/@NFpEogXySTuWExLvDQQHig/H1INdMJYD)
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chissa rivaldi
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October 27, 2020

Julia Fitness Landscapes Julia compatability package: https://github.com/JuliaLang/Compat.jl https://github.com/glesica/NKLandscapes.jl ^old, broken package that we're going to try to use today Installation using package manager in julia fails (NKLandscapes not found) Installation through github - fails

10/27/2020
October 15, 2020

Last day of RNA seq in julia Practical Ten -use kmeans or hclust (however many clusters you want) -Distance matrix from practical 4, use MDS from Multivarate Stats on this matrix -Use same matrix with clustering, color according to cluster https://juliastats.org/Clustering.jl/stable/kmeans.html add Clustering package

10/15/2020
RNA Seq with Julia

Class 10/6/20 Goal: Build counts table and analyze expression data in Julia https://biojulia.net/GenomicFeatures.jl/v0.2/io/gff3/ log on to CRC Make new working directory for today and cd into it copy files for today cp /tmp/ND_ICG_OCT_6/* . module load julia

10/8/2020
RNA-seq count quantification with Salmon

The RNA-seq analysis we'll be doing today has a workflow like this: We're starting with the second to last step (Salmon), and then moving to R/Rstudio for the Differential Expression Analysis and Visualization. We definitely don't have the time in class to do everything you can do with RNASeq data, so there are some links at the bottom of this document that you can follow to tailor this workflow to your needs. To begin: Log on to the CRC Make a working directory for today and cd into it: mkdir SEP_29

10/1/2020
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