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1. General guides
Introduction to the command line
Windows Subsystem for Linux
Using Ubuntu through a Virtual Machine
File formats used in bioinformatics
2. Program guides
Augustus
BLAST
Bcftools
Bowtie
Bowtie2
Conda
Fasterq-dump
Fastq-dump
FeatureCounts
Htseq-count
OrthoFinder
SAMtools
SPAdes
sgRNAcas9
3. Scripts
Annotated SNPs filter
Annotating SNPs
Combining featCount tables.py
DE analysis edgeR script.R
Fastq-dump to featureCounts
Genome annotation script
Linux setup script
SNP calling script
UniProt downloader
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Bioinformatics Notebook on GitHub
3. Scripts
These are scripts that use the programs and file formats discussed in this project.
Table of contents
Annotated SNPs filter
Annotating SNPs
Combining featCount tables.py
DE analysis edgeR script.R
Fastq-dump to featureCounts
Genome annotation script
Linux setup script
SNP calling script
UniProt downloader