I have some RNA-Seq data and I'd like to align it to the physical genome and see which sections of chromatin are geometrically open and being transcribed. The data are already sequence-aligned, and every Google search I do for tools that might help ends up sending me down a rabbit hole. What computational tools have helped you?
Starting out with RNA data is great, since you already have fully spliced entities, despite being in a different dynamic regime.
As the chromatin landscape itself is dynamic and High throughput data exploration has only begun in the last decade, consider the following tools and results with care...
You may find the following tools helpful: