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gt-eval

Compare annotation files and show accuracy measures (prediction vs. reference).

gt eval reference_file prediction_file

-nuc

evaluate nucleotide level (memory consumption is proportional to the input file sizes) (default: yes)

-ltr

evaluate a LTR retrotransposon prediction instead of a gene prediction (all LTR_retrotransposon elements are considered to have an undetermined strand) (default: no)

-ltrdelta

set allowed delta for LTR borders to be considered equal (default: 20)

-v

be verbose (default: no)

-o

redirect output to specified file (default: undefined)

-gzip

write gzip compressed output file (default: no)

-bzip2

write bzip2 compressed output file (default: no)

-force

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 numbe r 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”.

Report bugs to <gt-users@genometools.org>.