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Data Analysis Tools

QuEST - ChIP-seq data analysis package

HOMER - Hypergeometric Optimization of Motif Enrichment -- ChIP-seq and Motif Discovery

Bowtie - An ultrafast memory-efficient short read aligner

Tophat - A spliced read mapper for RNA-Seq

Cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq

UCSC Genome Browser

Ensembl Genome Browser

CEAS - Cis Regulatory Element Annotation System - ChIP-chip peak data mining

Primer-BLAST - primer designing tool for qPCR and qRT-PCR

Recombineering - Bacterial Recombination System

DAVID - Database for Annotation, Visulatization and Integrated Discovery - Gene annotation

ConSite - Trascription factor binding site search

SOLiD Next Gen Sequencer

SOLiD Software Support

SEQanswers -- Forum for next gen sequencing users

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