default.fusionseqrc

# --------------------------------- This section is required ---------------------------------
# Location of the bowtie indexes of the human genome and the composite model
BOWTIE_INDEXES="/path/to/bowtie/Indexes" 
# the subdirectory of BOWTIE_INDEXES where the human genome is indexed by bowtie-build
BOWTIE_GENOME="hg18_nh"
# the subdirectory of BOWTIE_INDEXES where the composite model is indexed by bowtie-build
BOWTIE_COMPOSITE="hg18_knownGeneAnnotationTranscriptCompositeModel"

# Pointer to the program twoBitToFa part of the blat suite
BLAT_TWO_BIT_TO_FA="/path/to/blat/twoBitToFa" 
# Location and filename of  the reference genome in 2bit format (to be used by blat)
BLAT_DATA_DIR="/path/to/blat/Data/Dir"
BLAT_TWO_BIT_DATA_FILENAME="hg18.2bit"

# Location and name of the transcript composite model sequence and interval files
TRANSCRIPT_COMPOSITE_MODEL_DIR="/path/to/transcript/Composite/Model"
TRANSCRIPT_COMPOSITE_MODEL_FA_FILENAME="knownGeneAnnotationTranscriptCompositeModel.fa"
TRANSCRIPT_COMPOSITE_MODEL_FILENAME="knownGeneAnnotationTranscriptCompositeModel.txt" 

# location of the annotation files
ANNOTATION_DIR="/path/to/annotationFiles" 
# conversion of knownGenes to gene symbols, description, etc. 
KNOWN_GENE_XREF_FILENAME="kgXref.txt" 
# conversion of knownGenes to TreeFam
KNOWN_GENE_TREE_FAM_FILENAME="knownToTreefam.txt" 

# Location and filename of the ribosomal library
RIBOSOMAL_DIR="/path/to/ribosomal/Dir"
RIBOSOMAL_FILENAME="ribosomal.2bit"

# Used for gfr2bpJunctions
MAX_NUMBER_OF_JUNCTION_PER_FILE=2000000

# Used for gfrRibosomalFilter
MAX_FRACTION_HOMOLOGOUS=0.05
MAX_OVERLAP_ALLOWED=0.75

# Used for gfrSpliceJunctionFilter
MAX_FRACTION_SPLICES=0.05


# ----------------------- This section is optional: visualization tools -------------------------
# URL of the cgi directory on the web server
WEB_URL_CGI="http://cgiURL" 
# location of the data directory on the web server, as seen from the web server
WEB_DATA_DIR="/path/to/data" 
# URL of the data directory on the web server
WEB_DATA_LINK="http://dataURL" 
# Number of nucleotides flanking the region (for UCSC Genome Browser)
UCSC_GENOME_BROWSER_FLANKING_REGION=500 
# URL of the public website (non cgi)
WEB_PUB_DIR="http://publicURL" 
# Location of the structural data for Circos
WEB_SDATA_DIR="/path/to/structural/Data/Circos" 
# Location of Circos installation
WEB_CIRCOS_DIR="/path/to/circos"