Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of ‘color space’, and it maximizes usable data b...

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Detalles Bibliográficos
Autores principales: Ondov, Brian D., Varadarajan, Anjana, Passalacqua, Karla D., Bergman, Nicholas H.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639273/
https://www.ncbi.nlm.nih.gov/pubmed/18842598
http://dx.doi.org/10.1093/bioinformatics/btn512
Descripción
Sumario:Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of ‘color space’, and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well as ChIP-Seq. Availability: Executables, source code, and sample data are available at http://socs.biology.gatech.edu/ Contact: nickbergman@gatech.edu Supplementary information: Supplementary data are available at Bioinformatics Online.

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