MMR: a tool for read multi-mapper resolution.

ABSTRACT:

Motivation

Mapping high-throughput sequencing data to a reference genome is an essential step for most analysis pipelines aiming at the computational analysis of genome and transcriptome sequencing data. Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase but also has significant impact on the results of downstream analyses. We present the multi-mapper resolution (MMR) tool that infers optimal mapping locations from the coverage density of other mapped reads.

Results

Filtering alignments with MMR can significantly improve the performance of downstream analyses like transcript quantitation and differential testing. We illustrate that the accuracy (Spearman correlation) of transcript quantification increases by 15% wh

SUBMITTER: Kahles A 

PROVIDER: S-EPMC4795617 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature