Does anybody know if the tool GREAT from Stanford U. can be used for RNAseq differential expression analysis directly from BAM/bed files of the reads aligned from the two experimental conditions? Or is it better to run preprocess the data through another tool beforehand?
i believe GREAT is used for chip-seq data not RNAseq data, they seem to want you to upload two bed files, one bed file of significantly enriched regions from chip-seq and another of background. you would probably have to generate these by using a peak caller. From a brief glance, it seems like they take these regions and see if function of nearby genes are similar so I am not quite sure how you would use this with RNA-seq data since you would expect most peaks to be over exons