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).

Click here for Anton's QuEST tutorial

QuEST 2.4 is available. See link on the right.

New in 2.4:

Filtering of outlier regions based on control data
Support of more input formats (bowtie, Maq)

New in 2.3:

Use of fold-enrichment to normalize for the depth of sequencing, size of the genome, and expectation of tag distribution under uniformity. This makes selection of peak calling parameters more intuitive and results in more interpretable ChIP enrichment scores. Underlying algorithms have not changed over 2.2.

Improved in 2.2:

• q-values for peaks and regions
• Setting of boundaries of regions of enrichment
• UCSC browser track generation

New features in 2.0:

• automatic generation of UCSC genome browser tracks for both raw data, calculated enrichment profiles, and regions called by QuEST
• better handling of broad peaks that are due to larger regions of DNA-protein contact
• p-values and FDR estimates for each positive region and peak
• filtering of outlier regions such as those from repeats

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.

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

QuEST Downloads

Software Package
QuEST 2.4
(gzipped tar that includes readme, Oct 5 2009)

QuEST 2.3
(gzipped tar that includes readme, Jun 15 2009)
QuEST 2.2
(gzipped tar that includes readme, Apr 30 2009)
QuEST 2.0beta
(gzipped tar that includes readme, Jan 12 2009)
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 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)