Question: Problem Uploading Bam And Bai Files
0
Ann Holtz-Morris, M.S. • 80 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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modified 5.4 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
5.4 years ago by
Ann Holtz-Morris, M.S. • 80
