UCSC link using Galaxy to see RNA seq peaks

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1

Dear All,
how can I generate the UCSC link using Galaxy to see RNA seq peaks?
Thanks in advance
Greetings,

2

Hi @rizwan_rehman_rehimi

Things to check

  1. Does your dataset contain a database metadata attribute? Changing database/build (dbkey)

  2. Is that database supported by UCSC? That application will name the same attribute as dbkey. The listing of all can be found here: UCSC Genome Browser Downloads

  3. If both are true, then a link to UCSC is automatically generated. Click on the little graph icon in the dataset to find it. FAQ: Different dataset icons and their usage

Screenshot

dataset-to-ucsc-link
dataset-to-ucsc-link1074×792 134 KB

  1. Now, if your genome is not hosted by UCSC, you can still visualize the data using a local IGV instead. Tutorials for this are at GTN Materials Search (query=igv)

Hope this helps but you can ask more questions if something isn’t working or isn’t clear. Screenshots of your expanded dataset (to show the database metadata) would be helpful for this. :slight_smile: