Hello Susan,

A BAM file is in binary format. To understand this datatype, please see the documentation for the tools in the group "SAM Tools". To view the data in a human-readable text file, convert using the tool "BAM to SAM".

More information about the type:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/

The best way to view this data is in a viewer such as Trackster or one of the alternatives listed in the dataset's box. Once you have a database assigned, the options will be listed.

Hopefully this helps. It would be helpful to please direct questions to the mailing list so that our entire team & community can contribute to and benefit from replies,

Jen
Galaxy team

On 6/29/12 9:44 AM, Susan Hester wrote:

Hi,

Yes I am registered now. I ran the tutorial exercise on the Galaxy datset / Tophat and tried to view it gave me an error and said the BAM file was not a valid file for Win32.?

Any ideas?

Susan Hester, Ph.D.
Research Biologist
Systems Biology Branch
Integrated Systems Toxicology Division (ISTD)
National Health and Environmental Effects Research Lab
US Environmental Protection Agency
109 T.W. Alexander Dr.
MD-B143-06
Research Triangle Park, NC 27711
hester.susan@epa.gov

Jennifer Jackson ---06/29/2012 12:13:36 PM---Hello Susan, Are you still having problem with registration?

From: Jennifer Jackson <jen@bx.psu.edu>
To: Susan Hester/RTP/USEPA/US@EPA
Cc: galaxy-dev@lists.bx.psu.edu
Date: 06/29/2012 12:13 PM
Subject: Re: [galaxy-dev] (no subject)

Hello Susan,

Are you still having problem with registration?

Please try again, doing the following to register at the Galaxy main public instance.
- Start at: http://usegalaxy.org/
- This will take you to: https://main.g2.bx.psu.edu/
- On the top menu, far right, is the "User" menu. Click on this, there are two options, "register" is the second.

Best,

Jen
Galaxy team

On 6/28/12 1:51 PM, Susan Hester wrote:

Hi,

I'm trying to register in Galaxy on the public server and under the "user" tab "register" is greyed out? How do I register?

Susan Hester, Ph.D.
Research Biologist
Systems Biology Branch
Integrated Systems Toxicology Division (ISTD)
National Health and Environmental Effects Research Lab
US Environmental Protection Agency
109 T.W. Alexander Dr.
MD-B143-06
Research Triangle Park, NC 27711
hester.susan@epa.gov

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Jennifer Jackson
http://galaxyproject.org