Decoupling alignment strategy from feature quantification using a standard alignment incidence data structure

Choi, K.; Vincent, M. J.; Churchill, G. A.

doi:10.1101/2021.02.16.431379

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bioRxiv · 10.1101/2021.02.16.431379

Decoupling alignment strategy from feature quantification using a standard alignment incidence data structure

Choi, K.·Vincent, M. J.·Churchill, G. A.

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Abstract

SummaryThe abundance of genomic feature such as gene expression is often estimated from observed total number of alignment incidences in the targeted genome regions. We introduce a generic data structure and associated file format for alignment incidence data so that method developers can create novel pipelines comprising models, each optimal for read alignment, post-alignment QC, and quantification across multiple sequencing modalities. Availability and Implementationalntools software is freely available at https://github.com/churchill-lab/alntools under MIT license. Contactkb.choi@jax.org or gary.churchill@jax.org

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Choi, K., Vincent, M. J., Churchill, G. A.. 2021-02-16. Decoupling alignment strategy from feature quantification using a standard alignment incidence data structure. https://doi.org/10.1101/2021.02.16.431379

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