PeakFinder Locates peaks (cohesin binding sites) in yeast ChIP microarry data
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PeakFinder Tags

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PeakFinder Description

The PeakFinder application was developed to be a tool that locates peaks (cohesin binding sites) in yeast ChIP (Chromatin Immunoprecipitation) microarry data. PeakFinder is a genome visualization tool that searches microarray ratio data for "peaks". The peaks are found using a smoothed curve that can be chosen interactively. Nucleotide content using a specified moving window can be displayed along with the microarray results. The program is almost generic for any genome, but still has a few yeast-only parameters. Input Files: - GenomeIndex.dat file: coordinates tell the location of each chromosome within the genome. The centromere location is also specified. - "Feature Coordinates" Excel Worksheet: Columns A, B and C must be Name, Coord1, Coord2. The coordinates are genome coordinates for each feature. - "Ratios" Excel Worksheet with microarray data: Column A must be "INAME". The Ratio data is assumed to be in the last column. The feature "INAME" values must mach those specified in the Feature Coordinates worksheet. - Directory with nucleotide sequences, one file for each chromosome. The sequence data can be in fasta format with a defline, or simply an ASCII file. The names of the files must be chr* or chrNN*. For example, chr05.fsa, or chrviii_562639.ascii. Either "old" or "new" file format from the Saccharomyces Genome Database is acceptable. - PeakFinder.INI is in the directory C:\Documents and Settings\\Local Settings\Application Data\StowersInstitute\PeakFinder Output Files: - The chart is automatically placed on the clipboard, if the bitmap or metafile option is selected, and can be immediately pasted into any other application after it is displayed. (Unchecking the Auto Save Chart box stops this automatic placement of the chart on the clipboard). Otherwise, press the Save button on the Chart tabsheet to save the chart to a specified GIF file. - The Save Peaks button on the Peaks tabsheet can be selected to save a Peaks.csv file, which can be opened in Excel. - The "Process All" button on the RawData tabsheet results in a set of files being produced. Normally specify a new directory and it will contain these files when the processing is complete: RatioFileName.dat, RatioFilename-ChromosomeNN.gif (NN=01 to 16), and RatioFileName-Peaks.csv, where RatioFileName is the name of the Ratio Excel File specified on the Raw Data tabsheet.

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