Provided by: giira_0.0.20140210-2_amd64 
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]