SpliceJunctionsDatabaseParams (BioFSharp)

SpliceJunctionsDatabaseParams Type

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll
Parent Module: STAR
Base Type: obj
All Interfaces: IEquatable<SpliceJunctionsDatabaseParams> , IStructuralEquatable , IComparable<SpliceJunctionsDatabaseParams> , IComparable , IStructuralComparable

Union cases

Union case	Description
`FileChrStartEnd string list` Full Usage: `FileChrStartEnd string list` Parameters: Item : `string list`	path(s) to the files with genomic coordinates (chr tab start tab end tab strand) for the splice junction introns. Multiple files can be supplied wand will be concatenated. Item : `string list`
`GTFchrPrefix string` Full Usage: `GTFchrPrefix string` Parameters: Item : `string`	prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC genomes) Item : `string`
`GTFfeatureExon string` Full Usage: `GTFfeatureExon string` Parameters: Item : `string`	feature type in GTF file to be used as exons for building transcripts Item : `string`
`GTFfile string` Full Usage: `GTFfile string` Parameters: Item : `string`	string: path to the GTF file with annotations Item : `string`
`GTFtagExonParentGene string` Full Usage: `GTFtagExonParentGene string` Parameters: Item : `string`	GTF attribute name for parent gene ID (default "gene_id" works for GTF files) Item : `string`
`GTFtagExonParentGeneName string list` Full Usage: `GTFtagExonParentGeneName string list` Parameters: Item : `string list`	GTF attrbute name for parent gene name Item : `string list`
`GTFtagExonParentGeneType string list` Full Usage: `GTFtagExonParentGeneType string list` Parameters: Item : `string list`	GTF attrbute name for parent gene type Item : `string list`
`GTFtagExonParentTranscript string` Full Usage: `GTFtagExonParentTranscript string` Parameters: Item : `string`	GTF attribute name for parent transcript ID (default "transcript_id" works for GTF files) Item : `string`
`InsertSave SpliceJunctionsDatabaseSaveOptions` Full Usage: `InsertSave SpliceJunctionsDatabaseSaveOptions` Parameters: Item : `SpliceJunctionsDatabaseSaveOptions`	which files to save when sjdb junctions are inserted on the fly at the mapping step Item : `SpliceJunctionsDatabaseSaveOptions`
`Overhang int` Full Usage: `Overhang int` Parameters: Item : `int`	length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1) Item : `int`
`Score int` Full Usage: `Score int` Parameters: Item : `int`	extra alignment score for alignmets that cross database junctions Item : `int`

Static members

Static member Description

Static member	Description
`SpliceJunctionsDatabaseParams.makeCmd` Full Usage: `SpliceJunctionsDatabaseParams.makeCmd` Returns: `SpliceJunctionsDatabaseParams -> string list`	Returns: `SpliceJunctionsDatabaseParams -> string list`
`SpliceJunctionsDatabaseParams.makeCmdWith m` Full Usage: `SpliceJunctionsDatabaseParams.makeCmdWith m` Parameters: m : `MountInfo` Returns: `SpliceJunctionsDatabaseParams -> string list`	m : `MountInfo` Returns: `SpliceJunctionsDatabaseParams -> string list`


                
                  
                    
                      SpliceJunctionsDatabaseParams.makeCmd

Full Usage: SpliceJunctionsDatabaseParams.makeCmd

Returns: SpliceJunctionsDatabaseParams -> string list

Returns: SpliceJunctionsDatabaseParams -> string list


                
                  
                    
                      SpliceJunctionsDatabaseParams.makeCmdWith m

Full Usage: SpliceJunctionsDatabaseParams.makeCmdWith m

Parameters:

m : MountInfo

Returns: SpliceJunctionsDatabaseParams -> string list

m : MountInfo

Returns: SpliceJunctionsDatabaseParams -> string list