Creating a Trackster visualisation from a reference in your history
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 Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
Hi Graham, This tends to work best right now when the Custom build is created first, then the dataset is assigned to that build. Create the build under "User -> Custom Builds". Also - just pick one dataset to represent the genome ( fasta or len ) - fasta is a better choice when you have it. Sounds like you do, so use that. At this point watch the status as the Custom Build is created - that same page will note if it is "processing". Wait until that finishes before using it with Trackster. However, while it is processing, you can assign the "database" of your custom genome build to your datasets without any issues. When all is done processing and with the database assignments made, launch Trackster and see if this changes the outcome. If you still have problems, please let us know. Thanks! Jen Galaxy team On 1/23/14 3:49 AM, graham etherington (TSL) wrote:
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
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
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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?
Yes, it definitely is.
If so, what am I doing wrong?
This is a Galaxy bug which has been fixed in this commit: https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513fc563dd231516... We have a release coming up, so this fix will be included in the release and will make it to our public server soon. In the meantime, note that you can use the genome fasta file rather than the len file to create a custom build and everything should work. Thanks, J.
participants (3)
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graham etherington (TSL) -
Jennifer Jackson -
Jeremy Goecks