Hi Ann,

When loading a BAM dataset, there is no need to load the index, just the BAM file itself. Galaxy will generate the .bai and create a composite dataset.

For the problem with detection, my guess is that the file was not named with a ".bam" extension, making detection problematic. The other problems are likely derivatives of this, and the .bai problems are expected - distinct bai datasets are not supported. If it was named as .bam, or appears to be, this would be a very strange case. Maybe check that the file doesn't have a hidden extension on the server you are loading from?

If the extension .bam was not used, please try loading using it, just BAM file, and see if that works now - maybe switching to FTP if not already using that. An example of how to do this is in this screencast (the 4th example, FTP, loads a BAM file):

http://wiki.galaxyproject.org/Learn/Screencasts -> Get Data: Upload File

Hopefully this resolves the problem,

Galaxy team

On 7/3/13 11:04 PM, Ann Holtz-Morris, M.S. wrote:
I've searched the archives and cannot find my situation.  I have an Illumina MiSeq dataset with ~8 million reads that was aligned to the reference genome on the MiSeq machine.  (The machine uses BWA to allow overlapping reads, unlike Casava.) The alignment generated dataset.bam and dataset.bam.bai files in the same directlry.

I used Get Data to upload both files. The problems, possibly related, are that Galaxy 1) would not recognize the .bam file as a bam file and 2) would not recognize the dataset.bam.bai file as the bam file metadata.

After uploading the bam file, originally identified as a text file, I manually used the pen option to tell Galaxy that the data was a .bam file. I then uploaded the .bam.bai file. The data would not display the data at UCSC genome browser nor in Trackster, even though those options were displayed for the .bam file.  After uploading, I also used the pen editor to change from dataset.bam.bai to dataset.bai.

None of these options worked for Trackster, UCSC genome brower, nor IGV nor IGB. Interestingly, IGV would display it if the data was used directly form my hard drive but not through Galaxy.

Any advice would be greatly appreciated.
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Jennifer Hillman-Jackson
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