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      UC Davis Bioinformatics Prerequisites Workshop

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Introduction
Intro to the Workshop and Core
Getting Connected
What is Bioinformatics/Genomics Perspective?
CLI Intro
Unix & the Command Line
Unix & the Command Line - Challenge Solutions
Environment Variables
Installing Simple Bioinformatics Software
Conda
Clusters & Modules
Advanced CLI
Git Basics
Advanced Command Line Topics
Advanced Challenge Solutions
Using Screen to Manage Multiple Projects (optional)
Intro to R
Introduction to R
Intro to tidyverse and ggplot2 - Prepare
Intro to tidyverse and ggplot2
Linear models in R
Spreadsheets
Working with spreadsheets
Bioinformatics
A Simple Bioinformatics Workflow
Support
Cheat Sheets
Software and Links
Scripts
ETC
Closing thoughts
Workshop Photos
Github
Biocore website

ADVANCED CHALLENGE SOLUTIONS

CHALLENGE 1

cat BSD | sed 's/ //g'

CHALLENGE 2

zcat C61_S67_L006_R1_001.fastq.gz | sed -n '2~4p' | cut -c1-5 | sort | uniq -c

CHALLENGE 3

find /software/perl-libs/ -name "*.pm" | while read x; do grep -H -w -i blast $x; done

CHALLENGE 4

zcat C61_S67_L006_R1_001.fastq.gz | grep -E '[CTGN]A{7,16}$'

CHALLENGE 5

find -L /share/biocore/joshi/projects/genomes -maxdepth 7 -name "*.fa" | grep -E 'ce10|danRer7' | xargs wc -c | awk '$1<10000'