Abstract
SUMMARY: Next-generation sequencing can provide insight into protein-DNA
association events on a genome-wide scale, and is being applied in
an increasing number of applications in genomics and meta-genomics
research. However, few software applications are available for interpreting
these experiments. We present here an efficient application for use
with chromatin-immunoprecipitation (ChIP-Seq) experimental data that
includes novel functionality for identifying areas of gene enrichment
and transcription factor binding site locations, as well as for estimating
DNA fragment size distributions in enriched areas. The FindPeaks
application can generate UCSC compatible custom 'WIG' track files
from aligned-read files for short-read sequencing technology. The
software application can be executed on any platform capable of running
a Java Runtime Environment. Memory requirements are proportional
to the number of sequencing reads analyzed; typically 4 GB permits
processing of up to 40 million reads. AVAILABILITY: The FindPeaks
3.1 package and manual, containing algorithm descriptions, usage
instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks
Source files for FindPeaks 3.1 are available for academic use.
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