gaeval(1)
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
