The ViennaRNA TrackhubsWe built trackhubs for several of our studies to easily browser and vizualize our results.
How to use a trackhub
To load the data into UCSC genome browser, just follow this simple procedure:
- copy the link of one of our trackhubs listed here, e.g. http://rna.tbi.univie.ac.at/trackhubs/RNAz/RNAzhub.txt
- go to the Track Hubs page of the UCSC genome browser
- paste the link into the field "URL"
- click on the "Add hub" button
- click on the genome of your choice, e.g. "mm10"
- you now see the data of the trackhub in the UCSC genome browser window
- Below the browser window you will find the trackhub as a separate track section. Here you can further configure which subtracks to display and choose from a list of vizualisation modes
Genome wide RNAz screens
Mouse mm10 - 60way vertebrate alignments
link to trackhub: RNAz_mm10 track hub data in bed format: Download citation: RNA Structure Elements conserved between Mouse and 59 other Vertebrates. Thiel BC, Ochsenreiter R, Gadekar VP, Tanzer A, Hofacker IL (2018) Genes
This hub shows the location of conserved RNA structures loci in the mouse genome (mm10) using RNAz. It contains the following tracks, each of which lists several data subsets
- RNAzGenome: all RNAz loci and loci split into genomic partitions (genic, intergenic, intronic, exonic, etc.) based on gencode M17 annotation
- RNAzRepeats: loci in repeat regions of the UCSC genome browser repeats track with subsets by repeat class (SINE, LINE, LTR, etc.)