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
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):
Get Data: Upload File
Hopefully this resolves the problem,
On 7/3/13 11:04 PM, Ann Holtz-Morris,
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
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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