Question: How to upload my own BAM file to UCSC genome browsers?
1
gravatar for sustcyucw
22 months ago by
sustcyucw20
sustcyucw20 wrote:

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....

rna-seq • 1.7k views
ADD COMMENTlink modified 22 months ago by genecats.ucsc560 • written 22 months ago by sustcyucw20
2
gravatar for Vijay Lakhujani
22 months ago by
Vijay Lakhujani4.1k
India
Vijay Lakhujani4.1k wrote:

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

ADD COMMENTlink written 22 months ago by Vijay Lakhujani4.1k

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....

ADD REPLYlink written 22 months ago by sustcyucw20
1
gravatar for genecats.ucsc
22 months ago by
genecats.ucsc560
genecats.ucsc560 wrote:

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:

  • genome@soe.ucsc.edu for general questions
  • genome-mirror@soe.ucsc.edu for questions involving mirrors or gbibs
  • genome-www@soe.ucsc.edu for questions involving private data

ChrisL from the UCSC Genome Browser

ADD COMMENTlink written 22 months ago by genecats.ucsc560
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2093 users visited in the last hour