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MOTIVATION The explosion of next-generation sequencing data has spawned the design of new algorithms and software tools to provide efficient mapping for different read lengths and sequencing technologies. In particular, ABI's sequencer (SOLiD system) poses a big computational challenge with its capacity to produce very large amounts of data, and its unique(More)
SUMMARY We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is(More)
ACKNOWLEDGMENTS I would like to express my sincere thanks to my thesis advisor, Sridhar Mahadevan. Sridhar has been such a helpful advisor, and every aspect of this thesis has benefited from his guidance and support throughout my graduate studies. I also like to thank Sridhar for giving me great patience and support to explore many different ideas and(More)
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