Question: Uploading sequencing data from GEO to USCS Genome Browser
gravatar for carly.harro
3.8 years ago by
carly.harro0 wrote:


I am trying to upload ChIP seq and S/MAR-seq data from GEO to my UCSC genome browser session; however, when I add it to my custom tracks it only displays information for chr1 and my interest is in chr2. I downloaded the .bed files (http) on a Mac which I believe automatically decompressed them. Then uploaded the files through custom tracks. Am I missing anything?

sequencing chip-seq genome • 1.7k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by carly.harro0

So I was able to find peaks for both data sets in chromosomes other than chr1; however, there seem to be few peaks that show up in Genome Browser. Anyway to check whether it was a file upload error or if the data set just doesn't have many peaks available? Thank you.

ADD REPLYlink written 3.8 years ago by carly.harro0

Please edit the original post to add additional information or use ADD COMMENT/ADD REPLY when responding to existing posts.

ADD REPLYlink written 3.8 years ago by GenoMax96k

We need to know the file types you are trying to upload... chip peaks wont show up as peaks in a bed file (.bed) unless you make a signal track bedgraph file (.bdg). If you are happy to see blocks instead of peaks then stick to bed files (boring). Bed files and Bedgraph files are too big to be useful so needs converting to bigbeds (for bed files) or bigwigs ( for bedgraph files). Even then it will only take 1 chr at a time so you are better off with a "track hub". You host the bigbeds/bigwigs data on your own ftp/http server and load it as needed.... very fast.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by YaGalbi1.5k
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