Journal
BIOINFORMATICS
Volume 32, Issue 16, Pages 2528-2530Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btw206
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Funding
- Centre National de la Recherche Scientifique (CNRS)
- Agence Nationale de la Recherche (ANR)
- Institut National du Cancer (INCa)
- Commission of the European Communities
- Ligue Nationale contre le Cancer
- ANR iSPLICE [ANR-11-BSV8-0013]
- Agence Nationale de la Recherche (ANR) [ANR-11-BSV8-0013] Funding Source: Agence Nationale de la Recherche (ANR)
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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 such as ChIP-seq reads elongation, nucleosome midpoint piling strategy for positioning analyses, or the ability to subset paired-end reads by groups of insert size that can contain biologically relevant information.
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