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gaeval - Online in the Cloud

Run gaeval in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gaeval that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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