Hi, I have run RNA-seq on 4 human samples, and I'd like to look at the count number from each sample at regions where any of the sample has some read coverage (say, threshold of 5 reads). What is the best way to do this? It is basically to examine the differentially expression regions across the transcriptome, not just limited to known annotated regions. I having been trying to use IRanges and related packages, but things start to get hairy when come to cluster the reads, condense them (within certain bp range), back-track the identities. I also looked at Cufflink, but it does not seem to be for this purpose, isn't it? Any advice is highly appreciated.
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