gaeval - calculate coverage and intergrity scores for gene models
based on transcript alignments
gaeval [options] alignments.gff3 genes.gff3
[moregenes.gff3 ...]
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