I know this has been asked before but not in a few years and I was wondering if there is an update.
I have some ChIPseq data and managed to get it to the stage where I am happy with the quality and mapped the reads and called peaks. However now I am looking to do some downstream analysis and rather than just looking at selected genes of interest it would be good to be able to identify significant peak location to genes to create a gene list. Is there an automated tool for this in Galaxy?
Further, is it possible to then preform some kind of gene-ontology analysis to suggest functional groups for significantly enriched genes with nearby ChIPseq peaks?
I have seen this done in some papers with pipelines in the public galaxy server like Cistrome, but several of the tools, like "ChipToPeak" are no longer working?
Sorry for the list of questions. I have little experience but will teach myself as much as I can :)