6ec4a1ca46568d31a5deff763a261c269a31fad2 dschmelt Thu Apr 16 14:22:53 2020 -0700 Correcting missing tag No RM diff --git src/hg/htdocs/goldenPath/help/bam.html src/hg/htdocs/goldenPath/help/bam.html index c65f6bc..694cf6f 100755 --- src/hg/htdocs/goldenPath/help/bam.html +++ src/hg/htdocs/goldenPath/help/bam.html @@ -61,31 +61,31 @@
  • If the file URL ends with .bam and the BAM index file URL ends with .bam.bai, you can paste the URL directly into the custom track management page, click submit and view in the Genome Browser. The track name will then be the name of the file. If you want to configure the track name and descriptions or the URLs are not as described, you will need to create a track line, as shown below in step 7.
  • Construct a custom track using a single track line. The most basic version of the "track" line will look something like this: 
        track type=bam name="My BAM" bigDataUrl=http://myorg.edu/mylab/my.sorted.bam
    Again, in addition to http://myorg.edu/mylab/my.sorted.bam, the associated index file http://myorg.edu/mylab/my.sorted.bam.bai must also be available at the same location. If not, you can specify the URL with the - bigDataUrl=http://myorg.edu/mylab/my.sorted.bam.bai
    • + bigDataUrl=http://myorg.edu/mylab/my.sorted.bam.bai
  • Paste the custom track line into the text box in the custom track management page, click submit and view in the Genome Browser.

    • Parameters for BAM custom track definition lines

    All options are placed in a single line separated by spaces. In the example below, the lines are broken only for readability. If you copy/paste this example, you must remove the line breaks. Click here for a text version that you can paste without editing.

        track type=bam bigDataUrl=http://...
         pairEndsByName=. 
         pairSearchRange=N