Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level.

ABSTRACT:

Summary

With the advancements of high-throughput single-cell RNA-sequencing protocols, there has been a rapid increase in the tools available to perform an array of analyses on the gene expression data that results from such studies. For example, there exist methods for pseudo-time series analysis, differential cell usage, cell-type detection RNA-velocity in single cells, etc. Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators. Typically, the impact of using different read-alignment or unique molecular identifier (UMI) deduplication methods has not been widely explored. Assessments based on simulation tend to start at the level of assuming a s

SUBMITTER: Sarkar H 

PROVIDER: S-EPMC6612833 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature