Abstract
Chromatin-associated RNA (caRNA) is a newly identified class of RNA stably linked to chromatin and responsible for maintaining the higher order structure of euchromatic regions in an accessible form (Schubert et al., Mol Cell 48, 434-444, 2012). This section provides a pipeline of bioinformatic analysis for this specific type of RNA-Seq. It can be run locally by combining several scripts or be carried out on the Galaxy platform (Giardine et al., Genome Res 15: 1451-1455, 2005).