GAEVAL

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