<p>I have been asked by my supervisor to conduct an RNAseq without experimentally depleting the samples. However I am quite unsure regarding how much sequencing depth per sample I would require in order to map a decent percentage of the ORFs if I were to proceed this way.</p>

<p>Has anyone ever done RNAseq w/o depletion and with what results? Would you go on with it or should I make the case for depleting even though it's gonna be more expensive.</p>

<p>Thanks.</p>

CC BY-SA 4.0
2020-03-11T15:56:32.580Z
Hi and welcome, there's not enough information in your post to allow a comprehensive answer in my opinion. RNAseq of which species is quite key here.
M__
CC BY-SA 4.0
2020-03-11T21:15:42.197Z
Did they want you to do poly-A enrichment instead? What is the actual goal? What is the organism?
Devon Ryan
CC BY-SA 4.0
2020-03-12T09:27:43.583Z
Hi, I just realized I did not mention I am working with plant **endopythic bacteria**, so no chances of using poly-A enrichment. The species is _Acidovorax facilis_, with the goal of assessing differential expression when exposed to different root exudates.
Roberto Siani
<rna-seq>
RNAseq without depletion?
# RNAseq without depletion?

(Asked by: username_0 on 2020-03-11)

I have been asked by my supervisor to conduct an RNAseq without experimentally depleting the samples. However I am quite unsure regarding how much sequencing depth per sample I would require in order to map a decent percentage of the ORFs if I were to proceed this way.

Has anyone ever done RNAseq w/o depletion and with what results? Would you go on with it or should I make the case for depleting even though it's gonna be more expensive.

Thanks.

**Tags:** rna-seq
> **Comments:**
> **username_1**: Hi and welcome, there's not enough information in your post to allow a comprehensive answer in my opinion. RNAseq of which species is quite key here.  
> **username_2**: Did they want you to do poly-A enrichment instead? What is the actual goal? What is the organism?  
> **username_0**: Hi, I just realized I did not mention I am working with plant **endopythic bacteria**, so no chances of using poly-A enrichment. The species is _Acidovorax facilis_, with the goal of assessing differential expression when exposed to different root exudates.  

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## 0 answers

