Hi,

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 directory

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 administrator?

If so, what am I doing wrong?

Many thanks,

Graham