Creating A Trackster Visualisation From A Reference In Your History

Question: Creating A Trackster Visualisation From A Reference In Your History

4.9 years ago by

graham etherington (TSL) • 100 wrote:

Hi, Im struggling to figure out how to visualise a SAM file in Trackster as a normal user (i.e. without admin privileges). Ive tried both my local install and use galaxy.org. This is what Ive 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

bwa alignment • 1.4k views

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modified 4.8 years ago by Jeremy Goecks • 40 • written 4.9 years ago by graham etherington (TSL) • 100

4.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 4.9 years ago by Jennifer Hillman Jackson ♦ 25k

4.8 years ago by

Jeremy Goecks • 40

Jeremy Goecks • 40 wrote:

Yes, it definitely is. This is a Galaxy bug which has been fixed in this commit: https://bitbucket.org/galaxy/galaxy- central/commits/117fef56513fc563dd231516196cfd601c1635e2 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.

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