Core Applications

Launch these applications using the -jar option, for example, 'java -jar pathTo/T2/Apps/FileSplitter' .
Click the name to see the command line menu.

Cel File Apps
Cel File Quality ControlCalculates various QC statistics on groups of xxx.cela files, including hierarchical clustering. Renders and saves png virtual slides for outlier files.
Coordinate Extractor 1lqExtracts control and pm coordinates from a text 1lq file for use by CelFileQualityControl app. Also creates virtual cel files for each class for visualization using the VirtualCel app. Useful for confirming correct orientation.
Cel File ConverterConverts text cel files into serialized float[][] arrays (xxx.cela) for use by other TiMAT2 applications.
Hierarchical ClusteringVisually clusters serialized float[] (xxx.celp) arrays using a Pearson correlation coefficient. Good for QC.
CorrelateOutputs all pairwise correlations between serialized float[] (xxx.celp) arrays using a Pearson correlation coefficient as well as performing heirarchical clusters.
Cel ProcessorWalks through the TPMap object file fetching the PMMM intensity values, saves the float array to disk. Provides options for median scaling, quantile normalization and PM-MM transformation.
Virtual CelCreates image files for each text version '.cel' file provided. Useful for identifying chips in need of masking by the Cel Masker application.
Cel MaskerDraws a virtual cel file base on a text version 'xxx.cel' file. Problem areas can be circled, masked, and saved as text version 'xxx.cel' files.
Intensity PrinterPrints .sgr files for any serialized int array (i.e. the processed cel files, xxx.cela).
Convert Agilent DataParses Agilent two color tiling data files to tpmaps and cela files for processing in TiMAT2.
Convert Geo DataParses two color Gene Expression Omnibus data files to tpmaps and cela files.
Convert Nimblegen PAIR 2 CelaConverts Nimblegen PAIR text data file(s) to cela files for processing in TiMAT2.
TPMap Apps
Mummer MapperUses Mummer ( to map and filter a 1lq text file against a genome. 100x faster than the TPMap Oligo Blast Filter and recommended if you don't care about 1bp mismatches. For processing very large chromosomes, ie human chr2 or 3 but not any drosophila, mummer needs a 64 bit machine with lots of RAM.
TPMap Oligo Blast FilterBlasts each oligo against a genome. Counts the number of matches (exact matches and 1bp mismatches). Replaces the t/f orientation column in the TPMap file with this count. Reassigns the chromosomal coordinates. Writes two files: BlastScored, saves TPMap lines that have at least one exact match; BlastFiltered, saves only those TPMap lines that have one exact match. Provides statistics on the filtering.
TPMap ProcessorConverts a tpmap file into precomuted windows across each chromosome for use by other TiMAT2 applications.
TPMap SortSorts a TPMap by chromosome and start position. Use to sort the remapped TPMap file.
Filter TPMap By RegionsStrips any tpmap oligos not contained within one or more of the user defined regions.
Convert Nimblegen NDF 2 TPMapConverts a Nimblegen NDF text file to a tpmap.
Main T2 Apps
T2Launches many of the TiMAT2 applications based on a tab delimited parameter file to convert, normalize, split, and merge txt cel files before launching ScanChromosomes. Runs on one machine or in parallel on a cluster.
FDR Window ConverterAssociates an empirical FDR esTiMAT2e with each window provided mock IPs were performed.
Find Sub Binding RegionsFinds the highest average scoring intensity difference or ratio sub window, within an interval, typically 350bp. Also automatically picks binding peaks and binding regions.
Interval FilterFilters intervals by a variety of criteria into two files, pass or fail.
Interval GFF PrinterPrints a text GFF3 file to represent the Intervals.
Interval Graph PrinterPrints a .sgr file to represent the Intervals in Affymetrix's IGB.
Interval MakerMerges overlapping windows into intervals. Options are provided to set the minimum required overlap and minimum score needed for merging.
Interval PlotterDisplays a detailed picture for each interval with oligo intensity information, transcription factor binding sites, repeat regions, best windows, etc. Use as the final filter in deciding whether the Interval is reasonable. Also use to pick binding regions and binding peaks by clicking and dragging.
Interval Report PrinterGenerates a spreadsheet or detailed reports for the Intervals with an assortment of calculations.
Load Chip Set Interval Oligo InfoSimilar to Load Interval Oligo Info but works on data from multi chip set experiments.
Load Interval Oligo InfoFetches and saves oligo intensity information from processed cel files for each interval.
Make Chromosome SetsFor use with multi chip sets. MakeChromosomeSets takes directories of chip set directories containing split chromosome intensity files from the CelProcessor app and combines them into a master set of chromosome split intensity files for use by ScanChromosomes.
Merge Window ArraysConcatenates serialized Window[]s into one. Useful for combining chromosome specific Window array results from the Scan Chromosome application.
Multi Window Interval MakerMerges overlapping windows into intervals from multiple Window[] arrays/ multiple experiments. Options are provided to set the minimum required overlap and minimum score needed for each Window[] array for merging, as well as the minimum number of passing windows, ie 2 out of 3. Useful for combining replicas or different antibodies into composit Intervals when one doesn't want to process them as a pool.
Oligo Intensity PrinterPrints .sgr files for the intensity ratio and intensity difference for each oligo when given processed treatment and control cel files.
Overlap CounterSorts two sets of Intervals based on whether they overlap one another. Good for finding common sets of Intervals between say two different antibodies or excluding intervals found associated with controls.
Scan ChipUse to score windows of oligo intensities with a Wilcoxon Rank Sum test and a trimmed mean or pseudo median ratio test. Wraps Richard Bourgon's symmetric p-value test and John Storey's q-value multiple testing applications to convert window ratio scores into corrected p-values. Saves a variety of window and point sgr files for direct visualization to Affymetrix's IGB.
Scan ChromosomesSimilar to Scan Chip but works on chromosomes. Useful for processing multi chip sets, ie those where the genome is spread out over several chips, not just one.
Scan GenesExtracts treatment and control intensities for all exons in each gene. Calculates a simple median ratio and ranks the genes by expression.
Score IntervalsScores Intervals for hits to a transcription factor binding matrix, LLPSPM.
Set Number Interval MakerDetermines the threshold(s) needed to generate a set number of intervals, multiple score indexes accepted. Useful for stratifying your results into say top 125, 250, 500 ... regions.
Window ScannerCounts the number of windows that pass a range of score cutoffs. Use this info to calculate false discovery rates.
General Analysis Apps
Aggregate PlotterFetches point data contained within each region, zeros the coordinates, scales, sums, and window averages the values. Usefull for generating class averages from a list of annotated regions. Use a spreadsheet app to graph the results.
Find Neighboring GenesFNG takes a list of genes in UCSC Gene Table format and intersects them with a list of regions finding the closest gene to each region as well as all of the genes that fall within a given neighborhood.
Annotate RegionsUse to characterize what genes surround the binding regions and whether there is a bias in their distribution. Can be combine with programs like GOMiner to identify possible biological functions associated with ChIP Chip data. At present it works with Drosophila 4.0 annotation. Parsers for other gff annotation can be readily adapted.
Intersect RegionsPerforms an intersection analysis on lists of genomic regions, uses random regions matched for GC content, length, array interrogated regions, and chromosome to calculate an enrichment over random and p-value. Also generates a distance to nearest region distribution histogram.
Intersect ListsIntersects two lists (of gene names) and using randomization, calculates the significance of the intersection and the fold enrichment over random.
Parse Bars For Particular RegionsGiven a list of regions and a directory of graph files, will collect and print the associated scores. A p-value and fold enrichment for each region's score can be calculated using chromosome, length, # scores, and gc matched random regions.
Ranked Set AnalysisPerforms an intersection analysis on lists of ranked regions creating a visual box-line-box representation as well as a rank based % intersection graph.
Correlation MapsCM creates correlation maps from gene expression data to look for physical gene clusters (aka gene expression neighborhoods, chromosome territories).
Scatter PlotVery simple scatter plot and correlation coefficient calculator for huge int or float arrays. Use to estimate data reproducibility. For example, the correlation coefficient for two independent ChIP Chip experiments using the same antibody should be above 0.8 and preferably above 0.9. If not, optimization is needed.
Score ChromosomesScores a genome for hits to a transcription factor binding matrix, LLPSPM.
Score SequencesScores a multi-FASTA file of sequences for hits to a transcription factor binding matrix, LLPSPM.
Utility Apps
JQSubJQSub executes a given command line on the specified clusters via qsub. It provides extensive logging and tracking of your submission.
Primer 3 WrapperWrapper for the primer3 ( application. Extracts sequence, formats for primer3, executes, and parses the output to a spreadsheet. Useful for bulk qPCR primer picking. Yes, you do need to validate your results.
Bar 2 GrConverts files to text files.
Gr 2 BarConverts files to binary chromosome specific files. Very fast loading in IGB. Small size.
Sgr 2 BarConverts files to binary chromosome specific files. Very fast loading in IGB. Small size.
Tag 2 BarConverts signature sequencing xxx.bed files (tab delimited chr start stop etc) to binary chromosome specific stair-step/ heatmap files. Very fast loading in IGB. Small size.
Windows 2 Heat Map SgrConverts a text file containing four tab delimited columns (chr, start, stop, score) to a heat map compatible file for import into IGB.
Export Intergenic RegionsTakes a GFF file and exports regions not covered by any annotation, the intergenic regions.
Export Intronic RegionsTakes a UCSC gene table and exports the most conservative estimate of intronic sequence.
Best Window Score ExtractorFetches the best window for each given region from a serialized Window array.
Fetch Genomic SequencesGiven a file containing genomic coordinates, fetches and saves the sequence (column output: chrom origStart origStop fetchedStart fetchedStop completeFetch seq).
Oligo TilerTiles oligos across genomic regions returning their forward and reverse sequences.
File Cross FilterFCF take a column in the matcher file and uses it to parse the rows from other files. Useful for pulling out and printing in order the rows that match the first file.
File JoinerJoins many text files together, paying attention to avoid fusing the last and first lines from two files. Use to combine the remapped TPMap file.
File SplitterSplits a text file into many files given a number of lines, use to split the TPMap file for TPMapOligoBlastFiltering.
Print Select ColumnsSpread sheet/ tab delimited file manipulations.