Abstract
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.eduSupplementary information: Supplementary data are available at Bioinformatics Online.
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