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1 = Java Genomics Toolkit
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2
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3 This is a collection of applications for genomics data processing, primarily high-throughput next-generation sequencing. There is a particular focus on processing data in Wiggle format, since many other tools already cover SAM, BAM, FastQ, etc. However, Wiggle/BigWig formats provide a compact way to store numerical data resulting from ChIP-seq and MNase-seq experiments. Common computations provided in this toolkit include adding, subtracting, dividing, multiplying, log-transforming, averaging, Z-scoring, and Gaussian smoothing Wig files.
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4
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5 Tools may be run from the command-line, a simple Swing GUI, or from Galaxy (http://getgalaxy.org).
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6
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7 == Loading the Tools into Galaxy
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8
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9 TODO
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10
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11 == Using the ToolRunner GUI
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12
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13 TODO
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14
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15 == Command-Line Usage
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16
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17 Applications can be run on the command-line, and the toolRunner.sh script is provided for convenience. Calling any script without arguments will display the help, as well as the missing mandatory arguments:
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18
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19 $ > ./toolRunner.sh wigmath.AddWig
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20 $ Usage: <main class> [options] Input files
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21 $ Options:
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22 $ * -o, --output Output file
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23
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24 Mandatory arguments are denoted with a (*).
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25
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26 Other tools require more input:
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27
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28 $ > ./toolRunner.sh ngs.Autocorrelation
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29 $ Usage: <main class> [options]
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30 $ Options:
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31 $ * -i, --input Input file
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32 $ * -l, --loci Genomic loci (Bed format)
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33 $ -m, --max Autocorrelation limit (bp)
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34 $ Default: 200
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35 $ * -o, --output Output file
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36
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37 === Log transform a Wig file with base 2
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38
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39 $ > ./toolRunner.sh wigmath.LogTransform --input input.wig --base 2 --output output.log2.wig
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40
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41 == Java Genomics IO
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42
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43 Those wishing to write their own scripts may be interested in https://github.com/timpalpant/java-genomics-io, the toolkit upon which these applications are built. |
