Has anyone tried "star --readFilesManifest manifest.tsv" and then "featureCounts --byReadGroup" to quickly get gene quantification for multiple samples?
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8 months ago
Xianjun ▴ 290

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.

RNA-Seq STAR featureCounts • 658 views
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