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 *
http://screencast.g2.bx.psu.edu/usinggalaxy_upload/flow.html
Hopefully this resolves the problem,
Jen
Galaxy team
On 7/3/13 11:04 PM, Ann Holtz-Morris, M.S. wrote:
Hi,
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.
Ann
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