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.
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.
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