Guest lectures Flashcards
Ancient DNA, RNAseq, Long read sequencing, metagenomics and binning, Genomic epidomiology, Canser-seq
Ancient DNA:
What is a unique characteristic of ancient DNA (aDNA)?
It is usually heavily fragmented
Ancient DNA:
What is often a major challenge in analyzing aDNA?
Presence of modern DNA contamination
Ancient DNA:
What technique is crucial for authenticating aDNA sequences?
Analyzing post-mortem DNA damage patterns
Ancient DNA:
Why is endogenous DNA content important in aDNA studies?
Indicates the amount of DNA from the original organism
Ancient DNA:
What has been a major advancement in the field of aDNA research?
Use of Next-Generation Sequencing (NGS)
RNA-Seq:
What is the main purpose of RNA-Seq?
To analyze the expression levels of genes
RNA-Seq:
In RNA-Seq, what is the significance of a ‘count matrix’?
It shows the number of times each gene is sequenced
RNA-Seq:
Which of the following is a challenge in RNA-Seq data analysis?
Normalizing data for accurate comparisons
RNA-Seq:
What role does ‘differential expression analysis’ play in RNA-Seq?
It compares gene expression levels between conditions
RNA-Seq:
Why is ‘quality control’ important in RNA-Seq?
To ensure accurate and reliable sequencing data
Long Read Sequencing:
What is a key advantage of long-read sequencing over short-read sequencing?
Better accuracy for repetitive sequences
Long Read Sequencing:
What is one of the main challenges associated with long-read sequencing?
High error rate
Long Read Sequencing:
Which technology is known for providing long-read sequencing capabilities?
PacBio
Long Read Sequencing:
In the context of long-read sequencing, what is “phasing” used for?
Resolving haplotypes in a genome
Long Read Sequencing:
How does long-read sequencing benefit the study of structural variations in genomes?
It allows for better resolution of large and complex genomic rearrangements
Quantitative Metagenomics:
What is the primary focus of quantitative metagenomics?
Analyzing the genetic diversity in a microbial community
Quantitative Metagenomics:
What does ‘alpha diversity’ refer to in metagenomics?
Diversity within a single sample
Quantitative Metagenomics:
What is the significance of ‘rarefaction’ in quantitative metagenomics?
To normalize data for species richness
Quantitative Metagenomics:
In metagenomics, what does the Shannon index measure?
Species richness and evenness
Quantitative Metagenomics:
How is ‘beta diversity’ used in quantitative metagenomics?
To compare diversity across different environments
Metagenomics Binning:
What is the primary goal of metagenomic binning?
To categorize DNA sequences into groups representing individual species or taxa
Metagenomics Binning:
What is a common method used in metagenomic binning?
Composition-based binning
Metagenomics Binning:
How does abundance-based binning work in metagenomics?
By looking at the relative abundance of sequences across samples
Metagenomics Binning:
What challenge does metagenomic binning help to address?
Separating and categorizing complex mixtures of DNA from environmental samples
