Hi Jessica, We don't think you can do all of these steps in the Genome browser. However, the following may be useful to you:
A) Use a peak caller with the raw ChIP-Seq data to make peak calls; this would have to be done with peak calling software (see this previous mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2011-October/027472.html). B) Load these peak calls into the genome browser as a custom track (using bed format). C) Make gene calls from the ChIP-Seq peak data using the table browser. Use the table browser to create a custom track of the upstream and downstream regions of genes and intersect that with your ChIP-Seq peak data. This previous mailing list question explains how to make the custom track: https://lists.soe.ucsc.edu/pipermail/genome/2010-October/023862.html You can now export these gene calls from the table browser into the software of your choice and intersect them with gene calls made with your microarray data using the microarray significance analysis software of your choosing. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 3/19/12 1:13 PM, Jessica Monteith wrote: > I would like to do a table search by intersecting two custom tracks that I > have loaded onto the browser. One of the tracks is a microarray data set > and the other is a p53 ChIP-Seq data set. I want to do an overlap so I can > identify regions where I have binding in the ChIP seq dataset and > upregulated gene expression. Is there a way I can change the parameters of > the search to expand the region that is included in the overlap? In my ChIP > seq data set, I often see p53 binding several Kb upstream of the TSS, so > that wouldn't necessarily overlap with the transcript in the track from the > microarray data. > Any help would be appreciated. Thanks. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
