One typical workflow for RNA-seq is to run STAR on the individual sample and then call htseq-count or featureCount to get the read count per gene. Recently I noticed that STAR has an option --readFilesManifest manifest.tsv that you can map multiple samples in one run and generate one BAM file with reads group tag @RG to mark individual samples, then you can run featureCounts −−byReadGroup on the BAM file to separate the multiple samples into individual read count profiles. I am not sure if this is a faster and more efficient way to run on multiple samples (than looping thru individual files). Has anyone tried it? Love to hear feedback. Thanks.