MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data.

ABSTRACT:

Motivation

Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms.

Results

In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduc

SUBMITTER: Ramachandran P 

PROVIDER: S-EPMC3570216 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature