A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.

ABSTRACT:

Motivation

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is widely used in biological research. ChIP-seq experiments yield many ambiguous tags that can be mapped with equal probability to multiple genomic sites. Such ambiguous tags are typically eliminated from consideration resulting in a potential loss of important biological information.

Results

We have developed a Gibbs sampling-based algorithm for the genomic mapping of ambiguous sequence tags. Our algorithm relies on the local genomic tag context to guide the mapping of ambiguous tags. The Gibbs sampling procedure we use simultaneously maps ambiguous tags and updates the probabilities used to infer correct tag map positions. We show that our algorithm is able to correctly map more ambi

SUBMITTER: Wang J 

PROVIDER: S-EPMC2951085 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature