---
name: "giira"
section: "1"
platform: "linux"
package: "giira"
version: "0.0.20140625-2"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/giira"
---

# giira(1)

Gene Identification Incorporating RNA-Seq data and Ambiguous reads

## 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** \[-a=is\_-t=5,-N\_-n=5\]