Manual for Triplex Target Analysis

Triplex-Inspector: Input | First Aid | Parameters | Output

Triplex-Inspector Manual

Triplex-Inspector is a command line program that can be excecuted from within the triplex-inspector folder.

Usage: run_inspector.sh -l "localConstraints" -o "offTargetConstraints" -c chromatinData -f chromatinFormat -a annotation -g genome -u ucscGenomeAssembly -s genomeSize -m maximalTargets -1 lociOfInterest.bed -2 alternativeLoci.bed -T Triplexator -B BEDtools -C Circos -v <outputdirectory>

First Aid

to get a brief usage description of Triplex-Inspector type:
    >./run_inspector.sh

Parameters

   <outputdirectory>
where you expect to find the result files
  [ -l "localConstraints" ] 
a quoted string containing any options to pass to Triplexator for assessing the loci of interest for putative target sites. See
Triplexator manual for specifics.
  [ -o "offTargetConstraints" ] 
a quoted string containing any options to pass to Triplexator for assessing off-targets (e.g. relaxing size and mismatch constraint). See Triplexator manual for specifics. If not provided the parameter set for the primary target search will be used (localConstraints).
  [ -1 BED-FILE ] 
loci of interest - full path to a bed file specifying the loci of interest
  [ -2 BED-FILE ] 
alternative loci - full path to a bed file specifying all loci to be considered in the off-target analysis. If not specified the whole genome is used.
  [ -c FILE ] 
chromatin data - full path to the file containing the chromatin organization data (e.g. DNase I cutsites)
  [ -f bigwig|bam ] 
chromatin format - the file format of the chromatin data (bam or bigwig)
  [ -g FASTA-FILE ] 
genome - full path to a fasta file containing the genomic sequence data
  [ -u STRING ] 
UCSC genome assembly - e.g. hg19
  [ -s FILE ] 
genome size - full path to a file the chromosome sizes in tab-separated format,
e.g. 'chr1 249250621'
  [ -m NUMBER ] 
maximal targets - maximal number of primary target clusters to be checked for off-target occurences. This is a failsafe to prevent intensive computation but instead allows to inspect the target clusters and tune respective parameters.
  [ -T TRIPLEXATOR ] 
path to Triplexator executable
  [ -B BEDtools ]
path to the folder containing BEDtools executable with terminal directory delimiter (i.e. "/"). If no path is given BEDtool binaries are expected to be found in the PATH variable.
  [ -C Circos ] 
path to Circos executable, if no path is given circos binaries are expected to be found in the PATH variable.
  [ -a GTF-FILE ] 
annotation data - full path to a gtf file specifying (gene) annotation data.
  [ -x ]
skips commands for which there already exists a result file (e.g. from a previous, disrupted run). This is to reduce runtime during debugging, but can result in undefined behavior.
  [ -v ]
print progress information (verbose).

OUTPUT

Triplex-Inspector populates the output directory with several files and folder while processing the given data. The main results that can be viewed in a browser are:
  • inspector_report.html - main result page
  • inspector_detail.html - detailed information for one particular target site
  • inspector_circos.html - summary page containing all generated circos plots
  • json/ - contains JSON-format data used to populate the datatables
  • img/ - contains the circos plots in png format
  • includes/ - contains css & image files as well as javascript libraries
  • FAQs.txt - Frequently Asked Questions
  • log.txt - the main log file
Other folders/files that contain partly raw output that are not accessed from the html report:
  • tts/ - putative primary target sites in the loci of interest (Triplexator output)
  • tfo/ - automatically generated TFOs used for off-target screening
  • tpx/ - (off-)targets matching the TFOs (Triplexator output)
  • circos/ - source scripts to generate one circos plot for each primary target region