1. Prepare a BAM file
  2. Submit a BAM file as custom track

Prepare a BAM file

The BAM format has been designed to represent read-alignment data which is usually in great amount. It is best made from/processed by the samtools. When aligning sequencing reads to genome, many aligners can output result in SAM format text files, which can then be converted to BAM file by samtools. When the BAM file is to be used as custom track, an index file must be available. The index file can also be made by samtools given the BAM file.

When you have BAM and its index file ready, place both of them on a web server at same directory. If the BAM file has name "xxx.bam", the index file must have name "xxx.bam.bai". In this way the BAM file is ready to be submitted as custom track to the Browser.

Submit a BAM file as custom track

Place your bigWig file on a web server, which has to be accessible by our Browser server. At control panel, go to "Tracks" → "Custom track", you can find custom BAM submission panel as following:

Replace the sample BAM file URL with your file URL, and assign a track name. Then you can click button to submit that track. Following is screenshot of the sample custom BAM track under name "aa bb" in "thin" mode:

The region under view is too large and too many reads are there. Zoom in to the large peak of reads, and change the mode to "full" to reveal details. Reads aligned to different strands are color differently, and mismatches are indicated by yellow vertical lines. Clicking on a read will display it's alignment:

Once the track is submitted, it will be registered in a table at upper position in control panel:


The custom BAM track function also supports BAM files with pair-ended read alignment data. Following is how that looks like via one example. Thin lines are used to join the two paired reads, which are in thin mode:


Last modifed: 09/27/2011