Question: Issue visualizing RNA-seq HISAT outputs in UCSC Genome Browser
gravatar for Ray_Enke
3 months ago by
USA/Harrisonburg, VA/James Madison University
Ray_Enke0 wrote:


I've used Galaxy to run HISAT alignments and Picard marked duplicates on my RNA-seq files. I usually visualize the .bam alignment outputs in the UCSC genome browser but option for viewing in UCSC is currently not available in my Galaxy history. IGV is currently the only option that I see. Does anyone know when the UCSC option will be restored?


ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by Ray_Enke0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There were some configuration changes between the two servers (UCSC main and Galaxy main), but those are now resolved.

If you are still having problems, maybe you need to assign the database metadata attribute to the BAM dataset?

Please be aware that only databases that are hosted by UCSC can be displayed there automatically by Galaxy's "display at UCSC main" link. Datasets will include the link if the database is a match for what UCSC refers to as the dbkey. To check if your genome is there, go to and review the available database/dbkeys -- the information will be noted in the landing page per-genome/release/build.

The "display with IGV" links operate the same way -- the database assigned in Galaxy needs to be an exact match for the IGV database. Some will be hosted on the public site and some will not be (this cannot be modified). But if needed, you can set up your own local IGV and either load the genomes that they have made available in the IGV resource bundles or you can load up your own custom genome IGV (and give it a "database" name that will match Galaxy's). Make sure the database names are the same between Galaxy/IGV or this will fail. The genome build/version matters -- to avoid problems try not to mix up builds (eg: mm9 with mm10). This may involve creating and assigning a Custom Build to the database in Galaxy. Also, be sure to have your local IGV open first (if used) before using the "IGV local" link or that will also lead to problems.

Galaxy FAQs:

IGV download/resources/support:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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