title: Deep sequencing of small chromatin-associated RNA: bioinformatic analysis.
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).
authors.affiliation: Biochemistry Centre, Universität Regensburg, Regensburg, Germany.
authors.forename: Sarah Daniela
authors.initials: SD
authors.lastname: Diermeier
authors.forename: Gernot
authors.initials: G
authors.lastname: Längst
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism*; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012342:RNA, Small Nuclear / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D002843:Chromatin; D012342:RNA, Small Nuclear