NAME

       joingenes - merge several gene sets into one

SYNOPSIS

       joingenes [parameters] --genesets=file1,file2,...  --output=ofile

DESCRIPTION

       This program works in several steps:

        1. divide the set of all transcripts into smaller sets, in which all transcripts are on
           the same sequence and are overlapping at least with one other transcript in this set
           (set is called "overlap")

        2. delete all duplications of transcripts and save the variant with the highest "score"

        3. if sequence ranges are set for some transcripts, the program detects, whether the
           distance to that range is dangerously close

        4. join:

           •   if there is a transcript dangerously close to one/both end(s) of a sequence range,
               the program creates a copy without the corresponding terminal exon

           •   if there is a transcript with start or stop codon in a set and a second one
               without this codon and they are "joinable", than this step joins the corresponding
               terminal exons

        5. selection: selects the "best" gene structure out of all possible "maximum" gene
           structures

           •   "maximum" gene structure is a set of transcripts from an overlap so that there is
               no other transcript in the overlap, which can be added to the set without
               producing a "contradiction"

           •   a gene structure is "better" than another one, if it has the transcript with the
               highest "score", which is not present in the other gene structure.

OPTIONS

   Mandatory parameters:
       --genesets=file1,file2,.../-g file1,file2,...
           where "file1,file2,...,filen" have to be data files with genesets in GTF format

       --output=ofile/-o ofile
           where "ofile" is the name for an output file (GTF)

   Optional parameters:
       --priorities=pr1,pr2,.../-p pr1,pr2,...
           where "pr1,pr2,...,prn" have to be positiv integers (different from 0). Have to be as
           many as filenames are added. Bigger numbers means a higher priority. If no priorities
           are added, the program will set all priorties to 1. This option is only useful if
           there is more than one geneset. If there is a conflict between two transcripts, so
           that they can not be picked in the same genestructure, joingenes decides for the one
           with the highest priority.

       --errordistance=x/-e x
           where "x" is a non-negative integer. If a prediction is ⇐x bases next to a prediction
           range border, the program supposes, that there could be a mistake. Default is 1000. To
           disable the function, set errordistance to a negative number (e.g. -1).

       --genemodel=x/-m x
           where "x" is a genemodel from the set {eukaryote, bacterium}. Default is eukaryotic.

       --alternatives/-a
           If this flag is set, the program joins different genes if the transcripts of the genes
           are alternative variants.

       --suppress=pr1,pr2,../-s pr1,pr2,...
           where "pr1,pr2,...,prm" have to be positive integers (different from 0). Default is
           none. If the core of a joined/non-joined transcript has one of these priorities it
           will not occur in the output file.

       --stopincoding/-i
           If this flag is set, the program joins the stop_codons to the CDS.

       --nojoin/-j
           If this flag is set, the program will not join/merge/shuffle; it will only decide
           between the unchanged input transcripts and output them.

       --noselection/-l
           If this flag is set, the program will NOT select at the end between "contradictory"
           transcripts. "contradictory" is self defined with respect to known biological terms.
           The selection works with a self defined scoring function.

       --onlycompare/-c
           If this flag is set, it disables the normal function of the program and activates a
           compare and separate mode to separate equal transcripts from non equal ones.

AUTHORS

       AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

ADDITIONAL DOCUMENTATION

       An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.

                                                                                     JOINGENES(1)