I’m struggling to figure out how to visualise a SAM file in Trackster as a
normal user (i.e. without admin privileges). I’ve tried both my local install
and use galaxy.org.
This is what I’ve done on usegalaxy.org:
Uploaded paired-end fastq sequences and a reference fasta file.
Mapped with BWA.
Clicked on SAM output – Visualize > Trackster
Chose 'View in new visualisation’, then ‘Add a Custom Build’.
In the ‘Add a Custom Build’ I give my build the name ‘solanum_reference’ and
the key ‘solanum_reference_1’. I select the fasta mapping reference from my
history under the ‘FASTA’ tab and under the Len File entry I upload a .len file
(tab-delimited) called ‘solanum_reference_1.len’.
I navigate back to my SAM history item, associate the Database/Build with my
new build (via the Edit attributes icon) and then again Visualize > Trackster >
View in New Visualization. I name the Browser, select my ‘solanum_reference’ as
the 'Reference genome build' and hit ‘Create’.
The view changes to the Trackster Browser and at the top I reads: "Preparing
data, This can take a while for a large dataset…..etc., etc. "
After a few minutes, this changes too: “Cannot display dataset due to an
error.” If I click on ‘View error’ I get:
Couldn't open /galaxy/data/chrom/solanum_reference_1.len , No such file or
Is it possible to create a custom build and use it to view a SAM file without
adding the .len and .2bit files in to the Galaxy file system as an
If so, what am I doing wrong?
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
Tel: +44 (0)1603 450601
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