Background:Single-cell RNA sequencing(scRNA-seq)technology is now becoming a widely applied method of transcriptome exploration that helps to reveal cell-type composition as well as cell-state heterogeneity for specif...Background:Single-cell RNA sequencing(scRNA-seq)technology is now becoming a widely applied method of transcriptome exploration that helps to reveal cell-type composition as well as cell-state heterogeneity for specific biological processes.Distinct sequencing platforms and processing pipelines may contribute to various results even for the same sequencing samples.Therefore,benchmarking sequencing platforms and processing pipelines was considered as a necessary step to interpret scRNA-seq data.However,recent comparing efforts were constrained in sequencing platforms or analyzing pipelines.There is still a lack of knowledge of analyzing pipelines matched with specific sequencing platforms in aspects of sensitivity,precision,and so on.Methods:We downloaded public scRNA-seq data that was generated by two distinct sequencers,NovaSeq 6000 and MGISEQ 2000.Then data was processed through the Drop-seq-tools,UMI-tools and Cell Ranger pipeline respectively.We calculated multiple measurements based on the expression profiles of the six platform-pipeline combinations.Results:We found that all three pipelines had comparable performance,the Cell Ranger pipeline achieved the best performance in precision while UMI-tools prevailed in terms of sensitivity and marker calling.Conclusions:Our work provided an insight into the selection of scRNA-seq data processing tools for two sequencing platforms as well as a framework to evaluate platform-pipeline combinations.展开更多
We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data analysis.GranatumX is inspired by the interactive webtool Granatum.GranatumX enables biologists to access the l...We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data analysis.GranatumX is inspired by the interactive webtool Granatum.GranatumX enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical environment.It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines.The architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various platforms.GranatumX can be run on the cloud or private servers and generate reproducible results.It is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench scientists.GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.展开更多
基金This work was supported by Strategic Priority Research Program of Chinese Academy of Sciences(Nos.XDB38050200 and XDA26040304).
文摘Background:Single-cell RNA sequencing(scRNA-seq)technology is now becoming a widely applied method of transcriptome exploration that helps to reveal cell-type composition as well as cell-state heterogeneity for specific biological processes.Distinct sequencing platforms and processing pipelines may contribute to various results even for the same sequencing samples.Therefore,benchmarking sequencing platforms and processing pipelines was considered as a necessary step to interpret scRNA-seq data.However,recent comparing efforts were constrained in sequencing platforms or analyzing pipelines.There is still a lack of knowledge of analyzing pipelines matched with specific sequencing platforms in aspects of sensitivity,precision,and so on.Methods:We downloaded public scRNA-seq data that was generated by two distinct sequencers,NovaSeq 6000 and MGISEQ 2000.Then data was processed through the Drop-seq-tools,UMI-tools and Cell Ranger pipeline respectively.We calculated multiple measurements based on the expression profiles of the six platform-pipeline combinations.Results:We found that all three pipelines had comparable performance,the Cell Ranger pipeline achieved the best performance in precision while UMI-tools prevailed in terms of sensitivity and marker calling.Conclusions:Our work provided an insight into the selection of scRNA-seq data processing tools for two sequencing platforms as well as a framework to evaluate platform-pipeline combinations.
基金This research was supported by grants from the National Institute of Environmental Health Sciences(NIEHS)through funds provided by the trans-NIH Big Data to Knowledge(BD2K)initiative(www.bd2k.nih.govGrant No.K01ES025434)+4 种基金the National Institutes of Health/National Institute of General Medical Sciences(NIH/NIGMSGrant No.P20 COBRE GM103457)the National Library of Medicine(NLMGrant No.R01 LM012373)the National Institute of Child Health and Human Development(NICHD,Grant No.R01 HD084633)awarded to LXG.
文摘We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data analysis.GranatumX is inspired by the interactive webtool Granatum.GranatumX enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical environment.It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines.The architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various platforms.GranatumX can be run on the cloud or private servers and generate reproducible results.It is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench scientists.GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.
