This is the command gt-eval 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
gt-eval - Compare annotation files and show accuracy measures (prediction vs. reference).
SYNOPSIS
gt eval reference_file prediction_file
DESCRIPTION
-nuc [yes|no]
evaluate nucleotide level (memory consumption is proportional to the input file sizes)
(default: yes)
-ltr [yes|no]
evaluate a LTR retrotransposon prediction instead of a gene prediction (all
LTR_retrotransposon elements are considered to have an undetermined strand) (default:
no)
-ltrdelta [value]
set allowed delta for LTR borders to be considered equal (default: 20)
-v [yes|no]
be verbose (default: no)
-o [filename]
redirect output to specified file (default: undefined)
-gzip [yes|no]
write gzip compressed output file (default: no)
-bzip2 [yes|no]
write bzip2 compressed output file (default: no)
-force [yes|no]
force writing to output file (default: no)
-help
display help and exit
-version
display version information and exit
The program shows sensitivity and specificity values for certain feature types (e.g.,
gene, mRNA, and exon). For some feature types the number of missing and wrong features of
that type is also shown. Thereby, “missing” means the number of features of that type from
the “reference” without overlap to a feature of that type from the “prediction”. Vice
versa, “wrong” denotes the number of features of that type from the “prediction” without
overlap to a feature of that type from the “reference”.
REPORTING BUGS
Report bugs to <[email protected]>.
Use gt-eval online using onworks.net services
