popgenomics / buc Goto Github PK

BUC project using the popPhyl dataset.


each directory contains two output files:
	*/output_summarized.txt: describes statistics measured for each loci.
	*/output_final_2.txt: contains averaged statistics found in output_summarized.txt, and correlations between some pairs of statistics.
 

The "./final_output.txt" file concatenates all of the */output_final_2.txt files.
It contains statistics measured in 103 species.

Can be read in R as follows:

	x = read.table("final_output_2.txt", h=T, sep="\t")

Contains:
	dataset: name of the directory
	NCBIname: NCBI names corresponding to the investigated species

	nLoci: number of retained loci (= contigs)
	Ltot: length of the coding frame for each loci

	GCtot: %GC for each loci
	GC12: %GC at positions 1 and 2 for each loci
	GC3: %GC at third position for each loci
	GCutr: %GC in UTR regions for each loci (utr3 and utr3: %GC if more than 20 nucl at the UTR3 and UTR5 positions respectively. utr if more than 20 nucl after concatenating UTR3 + UTR5

	_avg = average from the observed loci
	_std = standard deviation over the observed loci

	r_ = Pearson's correlation coefficient
	
	CorrectedExpression = mean number of mapped reads corrected by the %GC at positions 1 and 2

	Nc = Effective number of codons; estimated by using John Novembre's code ENCprime (ENc)
	Ncp = Effective number of codons by accounting for background nucleotide composition; estimated by using "ENCprime" (ENc')