DNA, Sequencing, and Gene Structure (Bioinformatics S3E3)
Channel: Danny Arends
Date: 2021-11-17

DNA sequencing data analysis steps, and structure of genes in prokaryotes and eukaryotes. This is a live-stream recording of the MSc and PhD lecture series: #Bioinformatics for plant and animal sciences, given digitally during the Covid19 pandemic at the Humboldt University in Berlin organized and lectured by Dr Danny Arends.

#Lectures @ https://dannyarends.nl/bioinformatik/
#Programming #Assignments and #Answers @ https://dannyarends.nl/bioinfo/
#Playlist: https://www.youtube.com/playlist?list=PLhR2Go-lh6X5A5WbiO3SPHuoWbwpNznUl

Chapters:
0:00 Welcome
0:51 Next generation sequencing and short reads
1:59 #NextGen #Sequencing relies heavily on Linux
3:08 Overview of a DNA sequencing pipeline
4:08 Read trimming and adapter removal
6:38 DNA sequence alignment to a reference genome
8:51 Handling read duplicates (optical / PCR artifacts)
10:48 SNP/INDEL realignment to improve mapping quality
15:00 Base recalibration based on known SNPs
16:16 Visualizing DNA sequencing alignments (IGV)
17:43 Novel variant calling and the variant call format (VCF)
23:53 DNA Sequencing is key to understanding biology
24:38 #GeneStructure in molecular biology
25:23 The structure of #prokaryote genes
29:19 The structure of #eukaryote genes
35:18 Difficulties to defining 'Gene'
36:57 Genes and encoded protein domains
37:51 Methods to detect genes in DNA sequencing data
39:35 Transposable elements AKA jumping genes

Thanks for taking an interest in my channel 😄 Subscribe and join me during my live streams Thursday afternoons on Twitch @ https://www.twitch.tv/dannyarends