Final Exam - Things to Memorize Flashcards
(21 cards)
YFS:
- common name
- genus
- species
- NCBI TaxonID
- number of haploid chromosomes
- haploid genome size
- common name: domestic dog
- genus: canis
- species: canis familiaris
- NCBI TaxonID: 9615
- number of haploid chromosomes: 39
- haploid genome size: 2.4 billion (Gb)
name the 3 key advancements in single cell technology
- integrated fluid circuits
- nanodroplets
- barcoding
draw the molecular techniques that allow us to achieve cell resolution
- cell barcode, UMI, sample index
- P5, 97
what molecular techniques that allow us to achieve cell resolution, why?
- cell barcode, UMI, sample index
- they allow you to identify the individual cell and differentiate the cells
what is the purpose of P5 and P7 adapters?
they are oligo binding sites for sequencing
nuclei advantages in single cell
- sample processing logistics
- less stress and mitochondrial signal
cell advantages in simple cell
- more complete transcriptions
- detection sensitivity
- better connection to translation
what are the four major downstream analyses of single cell transcriptomic data?
- differential expression
- gene enrichment analysis
- cell-cell communication
- trajectory analysis
mutations can be:
- harmful
- beneficial
- neutral
define sensitivity
trying to discover all the real variants
define specificity
limiting the false positives that creep in when filters get too lenient
how many probes does infintum 1 have, how many does infinium 2 have?
- infintum 1 = 2
- infinium 2 = 1
what are 2 metrics we use for looking for errors (QC) in SNPS?
- call rate per SNP (indicate genotype quality)
- call rate per individual (indicate DNA quality)
power is influenced by: (4 things)
- sample size
- distribution of effect sizes
- frequency
- linkage disequilibrium
telomere to telomere assembly recipe
- error correction of accurate long reads
- assembly graph construction
- graph simplification with ultra long reads
- phasing and scaffolding
We define the pangenome of based on 3 “A” components, what are they?
- Assemblies
- Alignments
- Annotations
pros and cons of low coverage WGS and high coverage exome
- WGS: pro=cost effective, con=less accurate variant calls
- exome: pro=more accurate variant calls, con=only sequencing 2% of the genome
what is the equation to determine the frequency of a variant in a general population?
1/2N
equation for false discovery rate
FDR= FP/FP+TP
what is the biological reason that explains how each individual can carry so many bad variant (in one word)?
redundancy
- what are the 4 things in gene regulation?
- what two are dictated by the cell?
- which two can be influenced by the researchers choices?
- what, when, where, and how much
- what and how much = cell
- when and where = researcher
