bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index 0a881120a18..bd4d3074a39 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -231,31 +231,31 @@ along with the rest of this example.

To create a custom track in this form, follow the below steps:

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 such as:
```
 chr14	95086227	95158010	ENSG00000100697.10	999	-	DICER1
    
```
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 here.
Download the helper programs expMatrixToBarchartBed and bedJoinTabOffset - from the utilities directory + from the utilities directory appropriate for your operating system.
Make sure the programs downloaded above are in your system's PATH variable. For example, if you downloaded the programs to your $HOME/Downloads directory, set your PATH variable accordingly:
```
 export PATH=$PATH:$HOME/Downloads
    
```

Now run expMatrixToBarchartBed (which in turn runs bedJoinTabOffset) like so:


 expMatrixToBarchartBed categoriesFile matrixFile bedInputFile outputBed

The argument outputBed will be a bed6+5 file, with the expCount, expScores, _dataOffset, and _dataLen fields computed for you, for example:


 chr14 95086227 95158010 ENSG00000100697.10 999 - DICER1 5 10.94,11.60,8.00,6.69,4.89 93153 26789
@@ -295,40 +295,40 @@
 expMatrixToBarchartBed or bedJoinTabOffset, run the program with no arguments 
 to get a usage message.
 
 
 
 Example #4
 
 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 here.
 
 
    If not already completed, follow steps 1-4 from Example 3 above, or
    download the example bed6+5 file here 
    Download the fetchChromSizes and bedToBigBed programs from the
-   utilities directory appropriate to your
+   utilities directory appropriate to your
    operating system.
    
Use fetchChromSizes to create a chrom.sizes file for the UCSC database you
    are working with (hg38 for these examples). Alternatively, you can download the 
    chrom.sizes file for any assembly hosted at UCSC from
-   our downloads page (click on "Full
+   our downloads page (click on "Full
    data set" for any assembly). For example, the hg38.chrom.sizes file for the hg38
    database is located at
-   http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
+   http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
    Save the autoSql file barChartBed.as to your computer.
    Run bedToBigBed to create the bigBarChart file:
    
 bedToBigBed -as=barChartBed.as -type=bed6+5 inputBed hg38.chrom.sizes output.bigBed
    
    Move the newly constructed bigBarChart file to a web accessible http, https, or ftp location.
    Construct a custom track line with a bigDataUrl parameter pointing to the newly created
    bigBarChart file. If the matrix and category files used to make the precursor barChart file
    are also moved to an http, https, or ftp location, we can point to them on the custom
    track line as well (all settings must be on the same line):
    
 track type=bigBarChart name="bigBarChart Example One" description="A bigBarChart file" 
 barChartBars="adiposeSubcut breastMamTissue colonTransverse muscleSkeletal wholeBlood" 
 barChartMetric=median barChartUnit=RPKM
 bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/barChart/hg38.gtexTranscripts.bb 
@@ -409,31 +409,31 @@
 collections based on metadata.
 The setting barChartFacets <column1,column2,...columnN> turns on the
 faceted selection on the track details and configure page which is useful for
 selecting which bars out of a large number to display by clicking designated checkboxes.
 The setting barChartStatsUrl <url> associates a table in tab-separated values
 with the barChart, with one line per bar. And the setting barChartMerge on
 enables a merge button inside of the faceted selections. It is particularly useful when
 there are many bars and many facets to condense a related group, such as tissue source.
 
 Below is an example track using these settings on source data for a
 Tabula Sapiens single cell RNA data from many tissues track.  This excerpt
 of settings from that track allows experimenting to see these settings in action, and to be
 loaded by going to the My Data, Custom Tracks page.
 -track type=bigBarChart  name="ex Tabula Sapiens" description="A bigBarChart using Tabula Sapiens data to illustrate new Details pages" visibility=pack barChartCategoryUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.categories barChartFacets=tissue,cell_class,cell_type barChartStatsUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.facets barChartMerge=on bigDataUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/tissue_cell_type.bb
+track type=bigBarChart  name="ex Tabula Sapiens" description="A bigBarChart using Tabula Sapiens data to illustrate new Details pages" visibility=pack barChartCategoryUrl=http://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.categories barChartFacets=tissue,cell_class,cell_type barChartStatsUrl=http://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.facets barChartMerge=on bigDataUrl=http://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/tissue_cell_type.bb
 
 
 Once loaded, click into an item to see the details page, in this case for the gene ACE2
 at the default position in hg38. On the details page, rather than a static bar chart
 image, there is a dynamic interactive selection screen with checkbox facets to narrow down
 the display. Adding barChartMerge on enables the display of the "merge"
 button, and barChartFacets tissue,cell_class,cell_type sources information in
 barChartStatsUrl ...tissue_cell_type.facets to enable the facet options.
 To interact with this example, click the first two "merge" buttons next to
 "tissue" and "cell_class."
 
   
 
 
 With those two merged selections, then click on the "Macrophage" option to see just
@@ -552,37 +552,37 @@
 
  track name="My singleCell barChart" type=bigBarChart bigDataUrl=https://hgwdev.gi.ucsc.edu/goldenPath/help/examples/barChart/singleCell/myTissueComp.bb
 
 -->
 Sharing your data with others
 
 If you would like to share your barChart/bigBarChart data track with a colleague, learn how to create a URL by 
 looking at Example 6 on this page.
 
 Extracting data from the bigBarChart format
 
 Because bigBarChart files are an extension of bigBed files, which are indexed binary files, it can 
 be difficult to extract data from them. UCSC has developed the following programs to assist
 in working with bigBed formats, available from the 
-binary utilities directory.
+binary utilities directory.
 
   
   bigBedToBed — converts a bigBed file to ASCII BED format.
   
   bigBedSummary — extracts summary information from a bigBed file.
   
   bigBedInfo — prints out information about a bigBed file. Use the -as option to see the file field descriptions.
 
 
 As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the 
 command line to view the usage statement.
 
 Troubleshooting
 
 If you encounter an error when you run the bedToBigBed program, check your input 
 file for data coordinates that extend past the end of the chromosome. If these are present, run 
 the bedClip program 
-(available here) to remove the problematic
+(available here) to remove the problematic
 row(s) in your input file before running the bedToBigBed program.