Hello Jianguang,
BAM files are indexed as part of the specification. But the content can vary with respect to read groups, samples, and other attributes.
The best advice is to review the SAM/BAM specification: http://samtools.sourceforge.net/samtools.shtml
Then examine the contents of the files by converting to SAM and/or running other tools found in 'NGS: SAM tools' or 'NGS: Picard (beta)' (or line command SAMTools) and compare against what your other tool expects. Next test a Tophat file with your tool and see if functions as expected - it might tell you if something is wrong and how to fix it. The tool authors of that tool would also likely be able be able to provide help - Tophat is a very common tool, they will be familiar with it.
Please note that when downloading a BAM file from Galaxy, the option to download the associated .bai file is also given. You will need both - so this means two downloads per BAM dataset: .bam and .bam.bai
The link to download large datasets can be obtained by right clicking the floppy disk icon inside a history item and choosing "Copy Link Address." for either. Once you have the link, use at a terminal prompt:
$ curl -O '<link>'
Good luck with your project,
Jen Galaxy team
On 9/13/12 1:05 PM, Du, Jianguang wrote:
Dear All,
I want to use the Tophat output files with ".accepted hits" to do analysis outside Galaxy. However, the program I am using requires the Tophat output to be indexed, sorted BAM files that contain headers. Do the Tophat ouputs with ".accepted hits" produced at Galaxy contain headers? Will the headers of BAM files generated by Tophat universally the same?
Thanks,
Jianguang
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