Collection of scripts that are useful for this course.
Contains scripts for the following tasks:
- Correct genome with mutations in
.vcffile:~/R/operations on genome/correctMutationFromVCFToFastaSequence.R - Translate nucleotide fasta according to annotation:
~/R/operations on genome/translateAnnotatedPseudogenesToProteins.R. - Visualize sets of peptides:
~/R/visualization/Pseudogene_peptides_comparison_and_visualization.R - Create upset diagram out of sets of peptides:
~/R/visualization/upset_diagram.R - Compare fasta sequence to detect if they are different:
~/Python/compare_sequence.py - Extract sequences from fasta file by ID e.g for a blast search
~/Python/extract_region_from_fasta.py - Filter vcf file for samples of interest and annotate the SNPs with gene IDs
~/Python/filtervcf_byInds_andAnnotate.py - Create a PCA using genotype data and color the points according to any phenotypic data column
~/R/genotype_PCA.r - Calculate nucleotide diversity and estimate upgma tree
~/R/Calculate_Diversity_And_Plot_A_Tree.R