Banana Slug Genomics

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.

Banana Slug Genomics Notes-
Chris Eisenhart 

Kevin's notes on fixing the wiki 
	Be more careful with meta-data, specifically the processing (FASTQC/preqc) results
		should be clearly linked to the data set they were made from.  
	More discussion regarding results
	Make a page for each data set that was collected, linking relevant information
	The wiki needs more information analysis, less information dump. (Look at the old data for examples)

Ed’s Lecture
	High-throughput sequencing techniques 
	Get DNA (Complex DNA sample) -> Adapter Ligation -> PCR amplification & sequencing
		Often techniques differ in PCR amplification & sequencing 
	Illumine Library Construction
		blunt end repair
		ligate adaptors 
		fill in adaptors 
		PCR amplification 
		Sequencing
			attach primers to either side of the target segment 
	Note that DNA can only be extended on the 3’ end (There is an -OH on the ribose at the 3’ end)
	PCR Biases 
		Shorter strands are more amplified 
		GC content 
	Often Fastq sequences come based on the tile where they were sequenced 
	3 pg is roughly 3 gig abases, therefore 1pg = 1gb 
		2pg = 1 banana slug genome
		1mg/2pg = 500,000 genomes
		there are 4 million 500 mers in a banana slug genome 
		2,000,000,000,000 total fragments for the MiSeq run
	Dilution parameter explanation
		Too dilute and not enough colonies form
		Too concentrated and colonies merge into each other, making sequencing impossible 
	Sequencing by synthesis
		Add a new base (flourescent tagged) and watch for the light 
	Limitations of Illumina Sequencing
		slow run time
		short reads 
		Fluorophore overlap
		Out-of-phase accumulation

Banana Slug Genomics

User Tools

Site Tools

Page Tools