GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

ABSTRACT:

Background

Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq experiments are larger and combining multiple experiments from sequence repositories can result in datasets with thousands of samples. Processing hundreds to thousands of RNA-seq data can result in challenges related to data management, access to sufficient computational resources, navigation of high-performance computing (HPC) systems, installation of required software dependencies, and reproducibility. Processing of larger and deeper RNA-seq experiments will become more common as sequencing technology matures.

Results

GEMmaker, is a nf-core compliant, Nextflo

SUBMITTER: Hadish JA 

PROVIDER: S-EPMC9063052 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature