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MMR: A tool for Read Multi-Mapper Resolution

View ORCID ProfileAndré Kahles, View ORCID ProfileJonas Behr, View ORCID ProfileGunnar Rätsch
doi: https://doi.org/10.1101/017103
André Kahles
1Computational Biology Center, Sloan-Kettering Institute, 1275 York Ave, New York, NY 10065, USA
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Jonas Behr
1Computational Biology Center, Sloan-Kettering Institute, 1275 York Ave, New York, NY 10065, USA
‡Current address: ETH Zürich, D-BSSE, Mattenstrasse 26, CH-4058 Basel, Switzerland
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Gunnar Rätsch
1Computational Biology Center, Sloan-Kettering Institute, 1275 York Ave, New York, NY 10065, USA
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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 multimapper 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 (Spear-man correlation) of transcript quantification increases by 17% when using reads of length 51. In addition, MMR decreases the alignment file sizes by more than 50% and this leads to a reduced running time of the quantification tool. Our efficient implementation of the MMR algorithm is easily applicable as a post-processing step to existing alignment files in BAM format. Its complexity scales linearly with the number of alignments and requires no further inputs.

Supplementary Material: Source code and documentation are available for download at github.com/ratschlab/mmr. Supplementary text and figures, comprehensive testing results and further information can be found at bioweb.me/mmr.

Contact akahles{at}cbio.mskcc.org and raetsch{at}cbio.mskcc.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 26, 2015.
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MMR: A tool for Read Multi-Mapper Resolution
André Kahles, Jonas Behr, Gunnar Rätsch
bioRxiv 017103; doi: https://doi.org/10.1101/017103
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MMR: A tool for Read Multi-Mapper Resolution
André Kahles, Jonas Behr, Gunnar Rätsch
bioRxiv 017103; doi: https://doi.org/10.1101/017103

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