Quantitative Enrichment of Sequence Tags: QuEST

QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).

QuEST 1.0 is available. See links on the right. Thanks to users who provided feedback on the beta.

E-mail QuEST's author, Anton Valouev. [Anton's home page]

QuEST is now published. See link on the right.

NOTE: we do not make precompiled versions available because of the large number of computational platforms we would have to support. You can compile QuEST easily if you have a standard installation of the gnu C compiler, which comes with most Linux systems. Mac users need to install the Developer Tools package (which comes with every system install disk but does not get installed by default). After you install Developer Tools, the C compiler will be in /usr/bin/gcc and the system will know where to find it.

QuEST Downloads

Software Package
QuEST 1.0
(gzipped tar that includes readme, Aug 18 2008)

QuEST test data (BIG FILES)
GABP ChIP Data
(gzipped text, 120.2 Mb, Mar 11 2008)
Control (RX-noIP) Data
(gzipped text, 271.4 Mb, Mar 11 2008)
Genome table
(gzipped text, small, Mar 11 2008)

Original QuEST Paper
Online Advance Publication at Nature Methods

QuEST data from the paper (BIG FILES)
Peak calls in QuEST format (text, small files, Aug 18 2008)
GABP
SRF
NRSF polyclonal
NRSF monoclonal
ChIP data (gzipped text, >100 Mb, Aug 18, 2008)
GABP (same as test data above)
SRF
NRSF polyclonal
NRSF monoclonal
Control (RX-noIP) Data (gzipped text, 271.4 Mb)