How to calculate A-statistic in an assembly?

hicham · 02-09-2010, 12:56 PM

Hi,

I have a problem and I can't find a solution to it anywhere.

In hawkeye (assembly visualisation sofware of Amos), we can see a graphic of "coverage stat" that correspond to the A-statistic parameter. I want to calculate this statistic in all points of the contig like in this softwtare.

I finded a PDF in internet that explaine how to calculate it:

A-statistic : Model the "arrival" of reads along the length of a unitig as a Poisson process:
G: length of genome
N: total number of reads
k: number of reads in the unitig
D : the distance between the start of the first read to the start of the
kth read

A-statistic = DN/G log (e) - k log (2)

Anyway, I can't applicate it in differents points of contig so that I can create a graphic.

Somebody can give me some explination or example to calculate it?

Thank you very much

02-09-2010, 12:56 PM	#1
hicham Junior Member Join Date: Feb 2010 Location: Malaga Posts: 8	How to calculate A-statistic in an assembly? Hi, I have a problem and I can't find a solution to it anywhere. In hawkeye (assembly visualisation sofware of Amos), we can see a graphic of "coverage stat" that correspond to the A-statistic parameter. I want to calculate this statistic in all points of the contig like in this softwtare. I finded a PDF in internet that explaine how to calculate it: A-statistic : Model the "arrival" of reads along the length of a unitig as a Poisson process: G: length of genome N: total number of reads k: number of reads in the unitig D : the distance between the start of the first read to the start of the kth read A-statistic = DN/G log (e) - k log (2) Anyway, I can't applicate it in differents points of contig so that I can create a graphic. Somebody can give me some explination or example to calculate it? Thank you very much