table of contents
GIIRA(1) | User Commands | GIIRA(1) |
NAME¶
giira - Gene Identification Incorporating RNA-Seq data and Ambiguous readsSYNOPSIS¶
giira -iG genomeFile.fasta -iR rnaFile.fastq -libPathDESCRIPTION¶
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]
February 2014 | giira 2014-02-10 |