NAME

       giira - Gene Identification Incorporating RNA-Seq data and Ambiguous reads

SYNOPSIS

       giira -iG genomeFile.fasta -iR rnaFile.fastq -libPath

DESCRIPTION

       GIIRA  (Gene Identification Incorporating RNA-Seq data and Ambiguous reads) is a method to
       identify potential gene regions in a genome based on a RNA-Seq mapping  and  incorporating
       ambiguously mapped reads.

OPTIONS

       -h : help text and exit

       -iG [pathToGenomes] : specify path to directory with genome files in fasta format

       -iR [pathToRna] : specify path to directory with rna read files in fastq format

       -scripts  [absolutePath]  :  specify  the  absolute  path  to the directory containing the
              required helper scripts, DEFAULT: directory of GIIRA.jar

       -out [pathToResults] : specify the directory that shall contain the results files

       -outName [outputName] : specify desired name for output files, DEFAULT: genes

       -haveSam [samfileName]: if a sam file already exists, provide the name, else a mapping  is
              performed. NOTE: the sam file has to be sorted according to read names!

       -nT  [numberThreads]  : specify the maximal number of threads that are allowed to be used,
              DEFAULT: 1

       -mT [tophat/bwa/bwasw] : specify desired tool for the read mapping, DEFAULT: tophat

       -mem [int] : specify the amount of memory that cplex is allowed to use

       -maxReportedHits [int] : if using BWA as mapping  tool,  specify  the  maximal  number  of
              reported hits, DEFAULT: 2

       -prokaryote  :  if  specified,  genome  is  treated  as  prokaryotic, no spliced reads are
              accepted, and structural genes are resolved. DEFAULT: n

       -minCov [double] : specify the minimum required coverage of the gene candidate extraction,
              DEFAULT: -1 (is estimated from mapping)

       -maxCov [double] : optional maximal coverage threshold, can also be estimated from mapping
              (DEFAULT)

       -endCov [double] : if the coverage falls below this value, the  currently  open  candidate
              gene  is  closed.  This  value  can  be  estimated  from the minimum coverage (-1);
              DEFAULT: -1

       -dispCov [0/1] : estimate (1) the coverage histogram for the read mapping, DEFAULT: 0

       -interval [int] : specify the minimal size of an interval between near candidate genes, if
              "-1" it equals the read length. DEFAULT: -1

       -splLim  [double] : specify the minimal coverage that is required to accept a splice site,
              if (-1) the threshold is equal to minCov, DEFAULT: -1

       -rL [int] : specify read length, otherwise this information is  extracted  from  SAM  file
              (DEFAULT)

       -samForSequential  [pathToSamFile]  :  if  it  is  desired  to  analyse  chromosomes  in a
              sequential manner, provide a chromosome sorted sam file  in  addition  to  the  one
              sorted by read names, DEFAULT: noSequential

       -noAmbiOpti : if specified, ambiguous hits are not included in the analysis

       -settingMapper  [(list  of parameters)] : A comma-separated list of the desired parameters
              for TopHat or BWA. Please provide

              for each parameter a pair of indicator and value, separated by  an  equality  sign.
              Note that parameters intended for the 3 different parts (indexing, aln, sam) of BWA
              have to be separated by a lowercase bar

              Example: -settingMapper [-a=is_-t=5,-N_-n=5]