--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)
--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.