Man pages sections > man1 > gaeval

gaeval - calculate coverage and intergrity scores for gene models based on

GAEVAL(1) User Commands GAEVAL(1)

NAME

gaeval - calculate coverage and intergrity scores for gene models based on transcript alignments

SYNOPSIS

gaeval [ options] alignments.gff3 genes.gff3 [moregenes.gff3 ...]

DESCRIPTION

Basic options:
-h|--help
print this help message and exit
-v|--version
print version number and exit
Weights for calculating integrity score (must add up to 1.0):
-a|--alpha: DOUBLE
introns confirmed, or % expected CDS length for single-exon genes; default is 0.6
-b|--beta: DOUBLE
exon coverage; default is 0.3
-g|--gamma: DOUBLE
% expected 5' UTR length; default is 0.05
-e|--epsilon: DOUBLE
% expected 3' UTR length; default is 0.05
Expected feature lengths for calculating integrity score:
-c|--exp-cds: INT
expected CDS length (in bp); default is 400
-5|--exp-5putr: INT
expected 5' UTR length; default is 200
-3|--exp-3putr: INT
expected 3' UTR length; default is 100
January 2016 gaeval 0.15.1