Upload Bam files

[David Bergenholm]

Hi,

I am trying to upload some bam files to the browser.

I use

track type=bam bigDataUrl= ftp://davidju:passW0rd@localhost:500/Hap1_1_1_trim_R_70.sorted.bam

and I get the error message: Error in TCP non-blocking connect() 111 - Connection refused. Host localhost port 500. Failed to open ftp://davidju:passW0rd@localhost:500/Hap1_1_1_trim_R_70.sorted.bam. If you are able to access the URL with your web browser, please try reloading this page.

And since I am able to access the data from other sites I wonder what is the cause of this?

 

Kind regards David

--

Mvh David Bergenholm (Jullesson), 
PhD Student                                        
Department of Biology and Biological Engineering
Division of Systems and Synthetic Biology

+46(0)703538155 (mobile)
david.j...@chalmers.se 

Chalmers University of Technology
Kemivägen 10
SE-412 96 Göteborg, Sweden
www.sysbio.se

 

 

[Matthew Speir]

Hi David,

Thank you for your question about uploading BAM files to the UCSC Genome Browser.

The issue is that you need to provide an actual web-accessible URL to the Genome Browser. The name "localhost" is not a valid website name, as it refers to "this" computer (more on localhost here: https://en.wikipedia.org/wiki/Localhost). This means that when you supply your localhost URLs to the UCSC Genome Browser, it then attempts to look for those on its local drive and since we don't have your files on our local machines, it spits back an error about not being able to find them.

What you need to provide to the Genome Browser is a web-accessible URL that can load your files from any computer. So something like "my.site.com/path/to/file.txt" or "my.labsite.edu/path/to/file.txt" or even the IP address of your server, such as "123.4.5.6/path/to/file.txt".

Your university may be able to provide some web-accessible space for your BAM files. Or, you can use the free, NSF-funded website CyVerse to host your files: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting. Note that if you do go with CyVerse you will need to add the "bigDataIndex" parameter to your track line to specify the URL to your ".bai" file.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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[David Bergenholm]

Thank you for your answer. 

I thought that the whole point with using ftp was that I could have the files locally. I will use some other method then. 

--

Mvh David Bergenholm (Jullesson), 
PhD Student    

Area of Advance PhD representative                                     

Department of Biology and Biological Engineering
Division of Systems and Synthetic Biology

+46(0)703538155 (mobile)
david.j...@chalmers.se 

Chalmers University of Technology
Kemivägen 10
SE-412 96 Göteborg, Sweden
www.sysbio.se

---

Från: Matthew Speir <msp...@soe.ucsc.edu>
Skickat: den 27 oktober 2017 20:37:34
Till: David Bergenholm; gen...@soe.ucsc.edu
Ämne: Re: [genome] Upload Bam files

 

[Brian Lee]

Dear David,

Thank you for using the UCSC Genome Browser and your interest to have bam files load locally.

You can successfully take this approach by acquiring a free for non-commercial use virtual machine image of the UCSC Genome Browser and launching it in the VirtualBox platform.

By running a this virtual machine on your laptop, you can then have data never leave your computer, as you would be running the entire Browser software on your own machine. Here is the Genome Browser in a Box (GBiB) help page that describes the process: http://genome.ucsc.edu/goldenPath/help/gbib.html

To run the GBiB you install VirtualBox and then you acquire the sizeable Browser image file from our store site. Once you have the GBiB up and running you can then share local folders on your computer with the virtual machine and Browse them, even offline entirely. We have recently added a European-based MySQL server (genome-euro-mysql.soe.ucsc.edu) that should automatically be detected when you start up your GBiB to help speed the display of data not included in the image (only a certain number of default assemblies and tracks are included in the image).

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UC Santa Cruz Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/1cdce205de794ffea9723ef6f9159609%40chalmers.se.

[David Bergenholm]

Hi,

Thanks for all your replies. I tried CyVers and it works great.

Thanks.