Man page - gaeval(1)

Packages contains this manual

Package: aegean
apt-get install aegean

Manuals in package:

Documentations in package:

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