Genes and geography -- a bioinformatics project скачать в хорошем качестве

Genes and geography -- a bioinformatics project

This is a full walkthrough of a bioinformatics project: Run PCA/TSNE on some population genotype data. 00:00 Intro 01:07 Hunting for data 04:55 Inspecting the VCF 06:02 Finding population labels for the samples 10:20 Parsing VCF with pysam 16:02 Going from alleles to numbers for a numpy array 21:47 When to work in colab versus python script 26:00 Saving data with pandas 28:42 Adding population labels from the panel file 33:33 To Colab! 36:54 PCA 40:17 First plot! Mission accomplished :) 42:03 Using Altair for plotting with labels 44:51 Second plot with population labels! 46:05 Merging with the igsr_population.tsv data 49:43 TSNE 53:36 Exercise: PCA on the SNPs 54:21 Conclusion and origin story for this project Download a VCF of population genotypes from the 1000 Genomes project. Use pysam to parse it and summarize it into a 2D numpy array to run PCA and save it as a pandas dataframe. Run PCA and tSNE on it and visualize the results with both matplotlib and Altair, coloring the points based on the ancestry labels. Here is the project ideas videos where I mentioned this project first:    • Bioinformatics project ideas   -- if you're interested in the origin story. All code including python script, download URLs for input files, and the Colab notebook: https://github.com/MariaNattestad/pca...