ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
UMass Chan Affiliations
Department of Biochemistry and Molecular PharmacologyDocument Type
Journal ArticlePublication Date
2013-10-01Keywords
*AlgorithmsInternet
RNA-Binding Proteins
Sequence Analysis, RNA
*Software
Biochemistry
Bioinformatics
Genomics
Molecular Biology
Metadata
Show full item recordAbstract
SUMMARY: Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus, identification of RNA-protein binding sites from high-throughput sequencing data presents unique challenges. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. AVAILABILITY: ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf.Source
Bioinformatics. 2013 Oct 1;29(19):2485-6. doi: 10.1093/bioinformatics/btt428. Epub 2013 Aug 8. Link to article on publisher's siteDOI
10.1093/bioinformatics/btt428Permanent Link to this Item
http://hdl.handle.net/20.500.14038/30260PubMed ID
23929032Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1093/bioinformatics/btt428