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giira - Online in the Cloud

Run giira in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command giira that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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]

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