How to upload my own BAM file to UCSC genome browsers?

Question

[sustcyucw]

http://genome.ucsc.edu/goldenPath/help/bam.html This is the workflow for generating a BAM custom track from UCSC website, but my problem is the Step5, about how to move both the BAM file and index file to an http, https, or ftp location.

The biggest problem is that I have web server but its access is limited in the Local Area Network, so the UCSC Genome Browser can't read my files....

Answer 1

[lakhujanivijay]

why not use IGV instead ? Look at this and this post!!

[sustcyucw]

Yeah I tried IGV first but I need to share the results with some one haven't install the IGV, so online genome browser can share just with the link....

Answer 2

[genecats.ucsc]

This sounds like the perfect use case for our GBiB product, it is a fully self-contained UCSC Genome Browser that runs on your own personal machine.

After downloading the machine, you can share a folder with your BAM file in it, and then view your BAM file just fine! It sounds like you already have a web server set up though, so you can just give the LAN url on the custom tracks page within your gbib and that should work as well.

The GBiB is free for personal and academic use, and can be downloaded from our genome-store.

If you have any questions about the GBiB please feel free to send a question in to our mailing lists:

• [e-mail] for general questions
• [e-mail] for questions involving mirrors or gbibs
• [e-mail] for questions involving private data

ChrisL from the UCSC Genome Browser