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 @ [ Ссылка ]
#Programming #Assignments and #Answers @ [ Ссылка ]
#Playlist: [ Ссылка ]
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
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