Genome Evolution and Diversity Lecture 1 Flashcards
what is illumina
sequencing method involving sticking DNA to a piece of glass, using probes, and then localised PCR which is then sequenced using fluorescence measures at each spot
preferred sequencing methods for functional genomics vs wgs
illumina used more for functional genomics
PACBIO is good for whole genomes- get a nice array of reads, overlapping bits etc
how does oxford nanopore work
looks at ion current changes, which are different depending on base
common genome sequencing arrangement currently
long reads assembled to generate a rough framework, short reads can then be used to generate the final, more accurate assembly
what technologies can look at base modifications?
pacbio and nanopore
RNA-seq
looks at what mRNAs are present, in what amounts etc
how does RNA-seq work
gets the RNA, removes any contaminant DNA, fragments and reverse transcribes it, amplification, sequencing as normal
how do you get actual data from RNA-seq?
aligning reads to transcripts- quantifies expression
what is a Q score
quality score, represents the probability of errors in bases- high = good
2 types of transcriptome assembly
de novo, reference assembly
drop-seq
creating ‘barcoded’ cells- allows you to get reads from individual cells by getting DNA bound to beads you can tell apart
combinatory indexing
plating cells and barcoding them, repeating that process until cells will all have individual combinations of barcodes
another method of barcoding
barcoded primers
why are single cell approaches used
-looking at single cell transcriptomes
-looking at chromatin accessibility in single cells
-combining approaches in single cells (this feels like genomics people yap)
