Question: How to upload my own BAM file to UCSC genome browsers?
1
gravatar for sustcyucw
2.4 years 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 • 2.1k views
ADD COMMENTlink modified 2.4 years ago by genecats.ucsc570 • written 2.4 years ago by sustcyucw20
2
gravatar for lakhujanivijay
2.4 years ago by
lakhujanivijay4.5k
India
lakhujanivijay4.5k wrote:

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

ADD COMMENTlink written 2.4 years ago by lakhujanivijay4.5k

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 2.4 years ago by sustcyucw20
1
gravatar for genecats.ucsc
2.4 years ago by
genecats.ucsc570
genecats.ucsc570 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 2.4 years ago by genecats.ucsc570
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