Question: RNA seq peaks
gravatar for jaganlakshman
4.6 years ago by
United States
jaganlakshman10 wrote:

how to visualize RNA seq peaks (what format) between different conditions in UCSC genome browser.

Say i have TopHat accepted hits as BAM file, can i visualize that as peaks in UCSC browser. I want it to visualize as peaks and not as alignments.



rna-seq • 3.1k views
ADD COMMENTlink modified 4.5 years ago • written 4.6 years ago by jaganlakshman10


Thanks for your previous mails, I have got the BigWig file Using the method described by you. And it works fine from public galaxy server. But i wanted to share the bigwig file to my colleague and i have downloaded the bigwig file and tried to upload the file in to ucsc browser. It throws out error like "you are trying to upload binary files directly", and not uploading.

Any way i can upload the bigwig file to UCSC genome browser? UCSC genome browser says bigwig files needed only to be supplied as URL. I dont understand it.



ADD REPLYlink written 4.5 years ago by jaganlakshman10

Yes, bigWig files are supplied to UCSC in custom tracks as a URL. The data itself it not loaded. You can just leave the data in Galaxy and use the "view at UCSC" link in the dataset's box to view it (no need to download). Or put the file on any other http server you may happen to have access to.

If you look at the help at the UCSC browser track descriptions are defined and how to customize custom tracks is described. 

Good luck! Jen, Galaxy team

ADD REPLYlink written 4.5 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Lakshman,

Here is how to perform the conversion for visualization:

  1. Convert the BAM to BedGraph format using "BEDTools -> Create a BedGraph of genome coverage"

  2. Compress the BedGraph to BigWig using "Convert Formats -> Wig/BedGraph-to-bigWig converter"

  3. Make certain the "database" attribute matches that of the target genome at UCSC you want to visualize the data in. The database should be the same as the one you mapped against in Galaxy.

  4. The link to "display at UCSC main" will appear in the dataset box.

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink written 4.6 years ago by Jennifer Hillman Jackson25k
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