aad054eb71ec975dc62cc94e4a2f030ed2de75e9 kuhn Mon Jun 24 13:35:39 2019 -0700 changed three instances of the word LIEK where it should have been SUCH AS or something else. LIKE is used when something is similar, but not identical. When you are giving an example of something it is not LIKE it, it =IS= it. Use some other construct diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index 20566c0..3b5e385 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -169,31 +169,31 @@ in that the order of names in the barChartBars field should exactly match the order of values from the expScores field in the bigBarChart file. </p> <a name="example3"></a> <h6>Example #3</h6> <p> In this example, you will use the helper scripts expMatrixToBarchartBed and bedJoinTabOffset on example matrix and category files in order to generate a bed6+5 barChart format file, which can be loaded as a custom track into the Genome Browser. </p> <p> The matrix file is a tab-separated (must be tabs, not spaces) file of the following form, perhaps resulting from an RNA-Seq analysis pipeline. Please note that the first line must describe each -column like in the example snippet below. +column as in the example snippet below. <pre> transcript sample1 sample2 sample3 sample4 sample5 ... transcriptName value1 value2 value3 value4 value5 ... </pre> </p> <p> The categories file then provides more meta information about this matrix file. It is a two column, tab-separated file that maps the samples in the matrix file to a specific category: <pre> sample1 category1 sample2 category1 ... ... sampleA category2 sampleB category2 @@ -204,31 +204,31 @@ </pre> <p> Each column in the first line of the matrix file must be found in the categories file. </p> <p> We have provided an example <a href="examples/barChart/exampleSampleData.txt">category file</a> and <a href="examples/barChart/exampleMatrix.txt">matrix file</a> to follow along with the rest of this example. <p> To create a custom track in this form, follow the below steps: <ol> <li>Create a bed6+1 file to use as a map for the items in your matrix (does not need to be - all-inclusive). This file, with example lines like: + all-inclusive). This file, with example lines such as: <pre><code> chr14 95086227 95158010 ENSG00000100697.10 999 - DICER1 </code></pre> will be one of three input files to the helper script expMatrixToBarchartBed. For an example file to follow along with the rest of this example, you can download an example bed6+1 file <a href="examples/barChart/hg38.gtexTranscripts">here</a>.</li> <li>Download the helper programs <em>expMatrixToBarchartBed</em> and <em>bedJoinTabOffset</em> from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe">utilities directory</a> appropriate for your operating system. </li> <li>Make sure the programs downloaded above are in your system's PATH variable. For example, if you downloaded the programs to your $HOME/Downloads directory, set your PATH variable accordingly: <pre><code> export PATH=$PATH:$HOME/Downloads @@ -257,31 +257,31 @@ bedJoinTabOffset matrixFile exampleBed6+3 outBed </code></pre></li> <li>Now that we have a bed6+5 format file that corresponds to the barChart format, we can construct a track line and prepend it to our bed6+5 file so the Genome Browser will recognize it: <pre><code> track type=barChart name="barChart Example" description="A barChart file" barChartBars="adiposeSubcut breastMamTissue colonTransverse muscleSkeletal wholeBlood" barChartMetric=median" visibility=pack </code></pre></li> <li>Use the upload button on the <a href="../../cgi-bin/hgCustom?db=hg38">custom track management page</a> for the human assembly hg38 to upload the file just created.</li> <li>Click the "submit" button.</li> </ol> <p> <em>expMatrixToBarchartBed</em> automatically computes the median values for all the samples in -the matrix file, which is useful when your experiment contains data from 8000 samples (like +the matrix file, which is useful when your experiment contains data from 8000 samples (such as the GTEx data). Furthermore, <em>expMatrixToBarchartBed</em> can compute the mean value of all samples in a category of the matrix file (instead of the default median), in addition to allowing for a specific ordering of the expScores field. NOTE: Set the barChartMetric setting to 'mean' if you use this option of <em>expMatrixToBarchartBed</em>. For more information about <em>expMatrixToBarchartBed</em> or <em>bedJoinTabOffset</em>, run the program with no arguments to get a usage message. </p> <a name="example4"></a> <h6>Example #4</h6> <p> In this example, you will use the bed6+5 file created in Example 3 to create a bigBarChart file, allowing the data to be remotely accessed and exist within a track hub. The track settings for bigBarChart on a hub can be viewed <a href="./trackDb/trackDbHub.html#bigBarChart">here</a>. </p>