Data Analysis of high throughput sequencing from WT, clb2-iml3 tetrads.

Sequencing platform :  Illumina HiSeq 2500
Image Analysis Pipeline : Illumina CASAVA_v1.8.0
Recombination analysis : ReCombine (Anderson et.al.,2011)

List of folders included:


SegFiles
________	Seg file lists the genotype of all four spores at each SNP position

file format : 	Chr | pos | "spaceholder" | sporeA | spore_B | spore_C | spore_D


SegPlots
________	Segregation profile of a tetrad. Each group of four rows represents a single yeast chromosome, indicated by a Roman numeral on the left. Each marker genotyped in all four spores is indicated by a blue or red line (blue = S288c, red = YJM789)


CrossOver_out
_____________	
		This folder holds the output file generated by the CrossOver program. CrossOver creates raw data files listing all individual events. It also produces a summary file listing key statistics, including the total CO and NCO count, average and median tract length for each type of GC, number of COs per chromosome, number of chromosomes lacking a CO, and several other parameters. CrossOver also contains built-in functions to analyze multiple aspects of CO regulation. Distances between adjacent events are produced by the program, including inter-CO distances; based on these distances, CrossOver calculates the gamma and beta parameters used to estimate the strength of CO interference. A file containing the distances from centromeres or telomeres to COs and/or NCOs is also automatically produced, which can be used to assess repression of recombination in those regions. CrossOver also calculates the ratio of adjacent COs

		The two most relevant output files are the "CoList" and "TractList" files which lists each Crossover and GC tract. The files include self- explainatory column headers.

		CrossOver program was used to analyze each genotype and two cutoffs: 0 kb and 5 kb. 

EventAnalysis
_____________	
		This folder contains analysis of CO and NCO types based on complexity
		of events and number of chromatids involved.
 
		Classification of CO and NCO as event types E1 through E7. 
		E1 = single NCO
		E2 = Single CO
		E3 = Single CO with a discontinuous GC
		E4 = Discontinuous NCO
		E5 = Ambiguous event involving two chromatids
		E6 = Ambiguous event involving three chromatids
		E7 = Ambiguous event involving four chromatids

		'allEventTypes.xls' is a detailed list of all events 
		'eventsPerTetrad.xls' includes number of events seen in each tetrad
		'E3toE7_groupDetails.xls' includes details for each grouped event. Each event has a unique identifier (group number) as Column 1
		'E3toE7_TractDetails.xls' includes information about each CO and NCO number in Column 1 corresponds to the group number in E3toE7_groupDetails.xls


		eventAnalysis_comparison.xlsx provides a comparison of all mutants analyzed