gaeval1
Calculate coverage and intergrity scores for gene models based on transcript alignments
Usage
gaeval [options]
alignments.gff3
genes.gff3
[moregenes.gff3 ...]
Overview
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
Releases
Unchanged in 5 releases since Debian 9 (Stretch).