LADiMIR is a stand alone Perl tool. That requirs Perl version 5.2 or above to run.
ladimir cLADfile miRNAfile GeneFile outputfile ladimir [-l cLAD file] [-m miRNA file] [-g Gene file] [-o Outputfile]
DESCRIPTION
Ladimir reads in cLAD,miRNA and gene files and from them analizes if miRNA's
lie within the cLAD regions and what genes lie up and downstream of each miRNA.
For the [name of outputfiles] no file extentions are needed.
Ladimir will create a file containing miRNA's that are within cLADS
And a .gff3 file with a list of miRNA that where used to do the comparison.
The options for the program are as follows:
-h -help Print this help file and exit
-o Create all output files in a specified directory.
The directory must exist as the program will not
create a new one. If not output name is give files
will be created wtih no name.
-l Specifies a non-default file which must containing
the cordinates for lamina associated domain (LAD's)
Valid format is bed.
-m Specifies a non-default file which must contain the
miRNA information. Valid formats are gff3, gff2 and gtf.
-g Specifies a non-default file which must contain the
gene information. Valid formats are gff3,gff2 and gtf.
-c Select a cut off distance for upstream and downstream genes.
If no number is specified then range is