Salmon provides fast and bias-aware quantification of transcript expression
Open Access
- 6 March 2017
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Methods
- Vol. 14 (4), 417-419
- https://doi.org/10.1038/nmeth.4197
Abstract
Salmon is a computational tool that uses sample-specific models and a dual-phase inference procedure to correct biases in RNA-seq data and rapidly quantify transcript abundances. We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA–seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure. It is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which, as we demonstrate here, substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis.This publication has 24 references indexed in Scilit:
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