I wat to view my dataset on UCSC browser. I know I am supposed to expand the dataset to see the “Display at UCSC browser main” option. But this option isn’t showing up at all. Please what might be the reason for this?
I have attached an image of the expanded dataset.
Thanks
Hi @lordtsage
click at Visualize icon (bar chart) to see links to UCSC browser and IGV.
Kind regards,
Igor
Thanks Igor,
I did this and found that the option to view on UCSC browser is available only for datasets uploaded from the browser. The other datasets I operated on do not throw up this option. Any idea what might be causing this?
Hi @lordtsage
Do you have dbkey (database value) assigned to datasets without link to UCSC browser? On the screenshot in your original post it is hg19. Galaxy uses dbkey value for communication with remote servers such as UCSC Genome Browser. A bit of background: when reads are mapped/aligned to a built-in genome, Galaxy assigns a proper dbkey to output files like BAM alignments, and the value propagate through downstream analysis. When a user uploads data, for example, intervals in BED format, the database (build) has to be specified manually either during upload or later via Edit Attributes (pencil icon) > select a proper value from Database/Build pull-down menu.
Hope this helps.
Kind regards,
Igor
Thank you so much Igor. You have been most helpful. I still have a little challenge, if you don’t mind. I have attached an expanded picture of the exon dataset which I got from UCSC database (BED format), and the operated dataset (tabular format). You can see that they both have the same database(hg18), which is as it should be. Do you think this problem is related to the difference in format? I can’t really know why this is acting up.
Hi @lordtsage
here the issue is in format: tabular does not work with the browser. It is too generic. Galaxy handles datasets based on labels (datatypes) assigned to files. For example, a BED file with txt, tabular and bed datatypes is treated differently: there is no columns in txt file, tabular is not compatible with the browser, hence no UCSC GB and IGV links.
Based on content on the first four columns, dataset #7 contains information about intervals. If it is BED, change the format (datatype) from tabular to bed: Edit attributes (pencil icon) > Switch to Datatype tab in the middle window and select an appropriate datatype in the pull-down menu.
Just in case: start positions in BED are zero based. Make sure you compensate for this in generic data manipulation.
Hope this helps.
Kind regards,
Igor
Yes!!! This definitely helps.
Thank you so much!
Regards,
Gabriel