Pasha: a versatile R package for piling chromatin HTS data. Homo sapiens

We describe an R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha (preprocessing of aligned sequences from HTS analyses) allows easy manipulation of aligned reads from short-read sequencing technologies (ChIP-Seq, FAIRE-seq, Mnase-Seq...) and offers innovative approaches to process and extract relevant information. Overall design: ChIP-seq using antibodies directed against the N-terminal region of Human RNA Polymerase II. An extended range of DNA fragments size was selected using linear acrylamide before library preparation and paired-ends sequencing.