One typical workflow for RNA-seq is to run
STAR on the individual sample and then call
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.