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Miseq Minimum number of RNAseq reads needed for comparison of bacterial stress v

RNAseq Single bacteria In-vitro minimum number of reads Miseq

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#1 Chris22

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Posted 26 May 2016 - 08:58 AM

Hello

 

I have a question about maximizing the number of samples that can be applied on a single MiSeq run.

 

I am working with a single anaerobic bacterial species, in vitro, and want to analyze the transcriptome response to H2O2 and atmospheric oxygen.

 

I have access to a single MiSeq run with a max of 20 million reads (150 paired end reads) and want to include as many variable conditions as I can.

 

The minimum number of samples is 2 (a control point vs a stress point) allowing 10 million reads for each.

 

But if I wanted to increase the number of timepoints for example (T1hr, 6hr, 12hr etc) with different adapters: how many "samples" can be run using a single 20million flowcell that will still produce useful and reliable depth of data for each sample?

 

 

Another way of asking this is: What is the minimum number of total reads (150 paired end reads) that I would need for reliable comparative bacterial transcriptome analysis between a control condition and a stress condition?

 

 

Thank you in advance,

 

Chris

 



#2 Trof

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Posted 02 June 2016 - 11:55 AM

From the little I know about RNA-seq you can never really tell. The transcript abundance varies, and also number of different transcripts varies from species to species, so the required coverage could only be guessed or estimated from prior experiments.
I found this, but that was done on HiSeq.

http://bmcgenomics.b...471-2164-13-734


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#3 Chris22

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Posted 14 July 2016 - 04:31 PM

Thank you for your reply and apologies for the delay. The paper you linked is very applicable to my experiments and I will update this link once I perform a trial using the miseq, for closure.







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