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Old 02-14-2020, 12:29 PM   #5
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Location: Michigan

Join Date: Aug 2019
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Default Resource for Bacterial RNA-seq depth recommendations

This paper "How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?" ( does a nice job of going through the key library prep and sequencing depth parameters for a bacterial RNA-seq experiment, and concludes that "5-10 million reads per sample [...] are sufficient for most applications of bacterial RNA-Seq".

From my experience, the critical experimental design question for a bacterial RNA-seq experiment is how well will the rRNAs be depleted (i.e.: how many reads will not be covering target genes) and how many replicates can I perform (i.e.: what will be my statistical power). Depth is helpful to overcome poor rRNA depletion but adding more replicates is the better use of increased sequencing cost, in my opinion.

Last edited by dmking; 02-14-2020 at 12:42 PM. Reason: Added additional notes for depth vs replicates
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