FusionSeq List of programs - Revision history

Asboner: /* gfrConfidenceValues */

2011-07-14T19:20:41Z

gfrConfidenceValues

← Older revision		Revision as of 19:20, 14 July 2011
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	Mapped_reads 236549456		Mapped_reads 236549456
	This represent the number of PE reads that were mapped. It is possible to determine this number by counting the number of lines in the [[#Mapped Read Format (MRF)\|MRF]] file. For example:		This represent the number of PE reads that were mapped. It is possible to determine this number by counting the number of lines in the [[#Mapped Read Format (MRF)\|MRF]] file. For example:
	grep -v AlignmentBlocks file.mrf \| wc -l		grep -v AlignmentBlocks file.mrf \| grep -v "#" \| wc -l

			A one-line command to generate this is:
			$ MAPPED=$(grep -v "AlignmentBlock" file.mrf \| grep -v "#" \| wc -l); printf "Mapped_reads\t%d\n" $MAPPED > file.meta

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Asboner: /* gfr2bpJunctions */

2011-04-05T18:06:02Z

gfr2bpJunctions

← Older revision		Revision as of 18:06, 5 April 2011
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	'''Usage''':		'''Usage''':

	gfr2bpJunctions <file.gfr> <tileSize> <sizeFlankingRegion> [minDASPER]		gfr2bpJunctions <file.gfr> <tileSize> <sizeFlankingRegion> <minDASPER>

	* Input: file.gfr - [[#Gene_Fusion_Report_(GFR)\|GFR]] file (not from STDIN)		* Input: file.gfr - [[#Gene_Fusion_Report_(GFR)\|GFR]] file (not from STDIN)
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	** tileSize: the number of nucleotides in each tile. For example, a 50nt read may be aligned to a 80nt junction, thus tileSize would be 40.		** tileSize: the number of nucleotides in each tile. For example, a 50nt read may be aligned to a 80nt junction, thus tileSize would be 40.
	** sizeFlankingRegions: the size, in nucleotides, of the flanking region around the exons.		** sizeFlankingRegions: the size, in nucleotides, of the flanking region around the exons.
	* Optional parameters:
	** minDASPER: the minimum DASPER values for which the breakpoint analysis is performed.		** minDASPER: the minimum DASPER values for which the breakpoint analysis is performed.

Asboner: /* geneFusions */

2011-02-17T11:20:06Z

geneFusions

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 ** none
 '''Note''': sample.mrf must include the sequences of the reads.
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Asboner: /* gfr2images */

2011-02-16T11:15:53Z

gfr2images

← Older revision		Revision as of 11:15, 16 February 2011
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	gfr2images < fileIN.gfr		gfr2images < fileIN.gfr

			* Pre-requisite: the pairCount column should be present in the [[#Gene_Fusion_Report_(GFR)\|GFR]] file. [[#gfrCountPairTypes\|gfrCountPairTypes]] should be executed first.
	* Inputs: [[#Gene_Fusion_Report_(GFR)\|GFR]] from STDIN		* Inputs: [[#Gene_Fusion_Report_(GFR)\|GFR]] from STDIN
	* Outputs: JPEG images labeled SampleID_0000#.jpg, where '''SampleID''' is the unique identification of the fusion candidate present in the [[#Gene_Fusion_Report_(GFR)\|GFR]] file.		* Outputs: JPEG images labeled SampleID_0000#.jpg, where '''SampleID''' is the unique identification of the fusion candidate present in the [[#Gene_Fusion_Report_(GFR)\|GFR]] file.

Asboner: /* Gene Fusion Report (GFR) */

2011-02-03T22:43:55Z

Gene Fusion Report (GFR)

Asboner: /* Gene Fusion Report (GFR) */

2011-02-03T22:35:55Z

Gene Fusion Report (GFR)

← Older revision		Revision as of 22:35, 3 February 2011
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	===Gene Fusion Report (GFR)===		===Gene Fusion Report (GFR)===
	This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:		This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:
	# ~~ID:~~ the ID of the fusion candidate: typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;		# the ID of the fusion candidate (''ID''): typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;
	# SPER, DASPER and RESPER: scoring of the fusion candidate;		# ''SPER'', ''DASPER'' and ''RESPER'': scoring of the fusion candidate;
	# Number of inter-transcript reads, i.e. the number of pairs having the ends mapped to the two genes;		# Number of inter-transcript reads (''numInter''), i.e. the number of pairs having the ends mapped to the two genes;
	# P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we computed the p-value for both directions: AB (where gene A is upstream of gene B) and BA (where gene B is upstream of gene A);		# P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we computed the p-value for both directions: AB (where gene A is upstream of gene B - ''pValueAB'') and BA (where gene B is upstream of gene A -- ''pValueBA'');
	# Number of intra-transcript reads for gene A and gene B, respectively, i.e the number of pairs where both ends map to the same gene;		# Mean insert-size value of the minimal fusion transcript fragment. As before for the p-values, we compute both ''interMeanAB'' and ''interMeanBA'';
	# The type of the fusion: cis, when both genes are on the same chromosome, or trans, otherwise;		# Number of intra-transcript reads for gene A (''numIntra1'') and gene B (''numIntra2''), respectively, i.e the number of pairs where both ends map to the same gene;
	# Name(s) of the transcripts: all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '\|';		# The type of the fusion (''fusionType''): cis, when both genes are on the same chromosome, or trans, otherwise;
	# Chromosome of the genes;		# Name(s) of the transcripts (''nameTranscript''): all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '\|';
	# Strand information;		# Chromosome of the genes (''chromosomeTranscript'';
	# Start and end coordinates of the longest transcript for both genes;		# Strand information (''strandTranscript'');
	# Number of exons in the composite model for both genes;		# Start and end coordinates of the longest transcript for both genes (''startTranscript'', ''endTranscript'');
			# Number of exons in the composite model for both genes (''numExonTranscript'');
	# Coordinates of the exons in the composite model: each exon is separated by the pipe symbol '\|' and start and end coordinates are comma-separated;		# Coordinates of the exons in the composite model: each exon is separated by the pipe symbol '\|' and start and end coordinates are comma-separated;
	# Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;		# Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;
	# ~~Inter~~-~~reads:~~ the ~~exon~~ and the coordinates of the reads ~~that join~~ the two genes. ~~Exon~~ number, start and end coordinates are reported as comma-separated, with the pipe symbol '\|' separating the different pairs;		# interReads: the pair-read type, as well as the exons and the coordinates of the reads joining the two genes. Pair-type, exon number, start and end coordinates are reported as a comma-separated list, with the pipe symbol '\|' separating the different pairs. The pair-reads type encodes the different possibilities two reads can be classified to in terms of the gene annotation set:
			#* 1 : exon-exon
			#* 2 : exon-intron
			#* 3 : intron-exon
			#* 4 : intron-intron
			#* 5 : intron-boundary
			#* 6 : exon-boundary
			#* 7 : boundary-exon
			#* 8 : boundary-intron
			#* 9 : boundary-boundary
	# Reads of the transcripts: the actual sequence of all the inter-reads.		# Reads of the transcripts: the actual sequence of all the inter-reads.
			# Pair-count: a summary of the number of reads for each category and joined exons (see interReads for the category definition). The field reports the pair-reads type, the number of reads, the two exons that are joined by the pair as a comma-separated list. The different pair types are separated by the pipe "\|" symbol.
	The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols and descriptions from the UCSC knownGene annotation set.		The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols and descriptions from the UCSC knownGene annotation set.
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Asboner: /* export2mrf */

2010-12-03T06:45:55Z

export2mrf

← Older revision		Revision as of 06:45, 3 December 2010
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	It generates an MRF file from the export files of a Genome Analyzer II run.		It generates an MRF file from the export files of a Genome Analyzer II run.

	'''Usage''':		'''Usage''':

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	==== gfrAddInfo ====		==== gfrAddInfo ====

Asboner: /* gfrAddInfo */

2010-12-03T06:45:42Z

gfrAddInfo

← Older revision		Revision as of 06:45, 3 December 2010
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	It includes additional information about the fusion transcript candidates such as gene symbols and gene description. This is a pre-requisite for [[#gfrBlackListFilter\|gfrBlackListFilter]] and [[#gfrAnnotationConsistencyFilter\|gfrAnnotationConsistencyFilter]].		It includes additional information about the fusion transcript candidates such as gene symbols and gene description. This is a pre-requisite for [[#gfrBlackListFilter\|gfrBlackListFilter]] and [[#gfrAnnotationConsistencyFilter\|gfrAnnotationConsistencyFilter]].

	'''Usage''':		'''Usage''':

Asboner: /* Mis-alignment filters */

2010-12-03T06:43:05Z

Mis-alignment filters

← Older revision		Revision as of 06:43, 3 December 2010
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	==Filtration cascade module==		==Filtration cascade module==
	===Mis-alignment filters===		===Mis-alignment filters===

			----

	==== gfrLargeScaleHomologyFilter ====		==== gfrLargeScaleHomologyFilter ====
	It removes potential fusion transcript candidates if the two genes are paralogs. It uses [http://www.treefam.org/ TreeFam] to establish is two genes have similar sequences.		It removes potential fusion transcript candidates if the two genes are paralogs. It uses [http://www.treefam.org/ TreeFam] to establish is two genes have similar sequences.

Asboner: /* Random pairing of transcript fragments */

2010-12-03T06:42:35Z

Random pairing of transcript fragments

← Older revision		Revision as of 06:42, 3 December 2010
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	==Random pairing of transcript fragments==		===Random pairing of transcript fragments===

			----

	==== gfrAbnormalInsertSizeFilter ====		==== gfrAbnormalInsertSizeFilter ====

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	===Combination of mis-alignment and random pairing===		===Combination of mis-alignment and random pairing===

			----

	==== gfrRibosomalFilter ====		==== gfrRibosomalFilter ====

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	===Other filters===		===Other filters===

			----

	==== gfrPCRFilter ====		==== gfrPCRFilter ====

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	===Scoring the candidates===		===Scoring the candidates===

			----

	==== gfrConfidenceValues ====		==== gfrConfidenceValues ====

← Older revision		Revision as of 22:43, 3 February 2011
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	===Gene Fusion Report (GFR)===		===Gene Fusion Report (GFR)===
	This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:		This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:
	# the ID of the fusion candidate (''ID''): typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;		# the ID of the fusion candidate (''id''): typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;
	# ''SPER'', ''DASPER'' and ''RESPER'': scoring of the fusion candidate;		# ''SPER'', ''DASPER'' and ''RESPER'': scoring of the fusion candidate;
	# Number of inter-transcript reads (''numInter''), i.e. the number of pairs having the ends mapped to the two genes;		# Number of inter-transcript reads (''numInter''), i.e. the number of pairs having the ends mapped to the two genes;
	# P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we ~~computed~~ the p-value for both directions: AB (where gene A is upstream of gene B - ''pValueAB'') and BA (where gene B is upstream of gene A -- ''pValueBA'');		# P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we compute the p-value for both directions: AB (where gene A is upstream of gene B - ''pValueAB'') and BA (where gene B is upstream of gene A -- ''pValueBA'');
	# Mean insert-size value of the minimal fusion transcript fragment. As before for the p-values, we compute both ''interMeanAB'' ~~and~~ ''interMeanBA'';		# Mean insert-size value of the minimal fusion transcript fragment. As before for the p-values, we compute both AB and BA versions (''interMeanAB'', ''interMeanBA'');
	# Number of intra-transcript reads for gene A (''numIntra1'') and gene B (''numIntra2''), respectively, i.e the number of pairs where both ends map to the same gene;		# Number of intra-transcript reads for gene A (''numIntra1'') and gene B (''numIntra2''), respectively, i.e the number of pairs where both ends map to the same gene;
	# The type of the fusion (''fusionType''): cis, when both genes are on the same chromosome, or trans, otherwise;		# The type of the fusion (''fusionType''): cis, when both genes are on the same chromosome, or trans, otherwise;
	# Name(s) of the transcripts (''nameTranscript''): all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '\|';		# Name(s) of the transcripts (''nameTranscript''): all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '\|';
	# Chromosome of the genes (''chromosomeTranscript'';		# Chromosome of the genes (''chromosomeTranscript'');
	# Strand information (''strandTranscript'');		# Strand information (''strandTranscript'');
	# Start and end coordinates of the longest transcript for both genes (''startTranscript'', ''endTranscript'');		# Start and end coordinates of the longest transcript for both genes (''startTranscript'', ''endTranscript'');
	# Number of exons in the composite model for both genes (''numExonTranscript'');		# Number of exons in the composite model for both genes (''numExonTranscript'');
	# Coordinates of the exons in the composite model: each exon is separated by the pipe symbol '\|' and start and end coordinates are comma-separated;		# Coordinates of the exons in the composite model (''exonCoordinatesTranscript''): each exon is separated by the pipe symbol '\|' and start and end coordinates are comma-separated;
	# Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;		# Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;
	# interReads: the pair-read type, as well as the exons and the coordinates of the reads joining the two genes. Pair-type, exon number, start and end coordinates are reported as a comma-separated list, with the pipe symbol '\|' separating the different pairs. The pair-reads type encodes the different possibilities two reads can be classified to in terms of the gene annotation set:		# interReads: the pair-read type, as well as the exons and the coordinates of the reads joining the two genes. Pair-type, exon number, start and end coordinates are reported as a comma-separated list, with the pipe symbol '\|' separating the different pairs. The pair-reads type encodes the different possibilities two reads can be classified to in terms of the gene annotation set:
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	# Reads of the transcripts: the actual sequence of all the inter-reads.		# Reads of the transcripts: the actual sequence of all the inter-reads.
	# Pair-count: a summary of the number of reads for each category and joined exons (see interReads for the category definition). The field reports the pair-reads type, the number of reads, the two exons that are joined by the pair as a comma-separated list. The different pair types are separated by the pipe "\|" symbol.		# Pair-count: a summary of the number of reads for each category and joined exons (see interReads for the category definition). The field reports the pair-reads type, the number of reads, the two exons that are joined by the pair as a comma-separated list. The different pair types are separated by the pipe "\|" symbol.
	The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols and descriptions from the UCSC knownGene annotation set.		The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols (''geneSymbolTranscript'') and descriptions (''descriptionTranscript'') from the UCSC knownGene annotation set.
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