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

@article{citeulike:3394239, 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.edu SUPPLEMENTARY INFORMATION: Available at Bioinformatics online.}, author = {Ondov, Brian and Varadarajan, Anjana and Passalacqua, Karla D D. and Bergman, Nicholas H H.}, citeulike-article-id = {3394239}, doi = {10.1093/bioinformatics/btn512}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {2gst, ngst}, month = {October}, posted-at = {2008-12-05 23:07:36}, priority = {2}, title = {Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.}, url = {http://dx.doi.org/10.1093/bioinformatics/btn512}, year = {2008} }

TY - JOUR ID - citeulike:3394239 L3 - citeulike-article-id:3394239 N2 - 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: Available at Bioinformatics online. JF - Bioinformatics (Oxford, England) SN - 1460-2059 TI - Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. KW - 2gst KW - ngst AU - Ondov, Brian AU - Varadarajan, Anjana AU - Passalacqua, Karla D AU - Bergman, Nicholas H PY - 2008/10/07/ UR - http://dx.doi.org/10.1093/bioinformatics/btn512 ER -