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Old 03-08-2011, 02:57 AM   #1
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Location: Frankfurt am Main, Germany

Join Date: May 2010
Posts: 2
Default Probability of sequencing low abundant transcripts from non-normalized library

Dear users,

I am new to this community and this is my first thread, I am also new to next generation sequencing analysis but I have interesting issue and I want to get some feedback from you. Thanks in advance for any replies!

Here is a scenario:
> non-normalized eukaryotic transcriptome library
> 3' Tag Sequencing; Reads of 100nts length; Illumina HiSeq 2000 Single Reads Machine

Two sequencing Attempts:
1) 50 Million Reads at one run with starting RNA consentration X
2) 3 Runs with respectively 10MilReads, 20MilReads, 20 MilReads with starting RNA concentration X

The RNA concentration is the same in the sample before any of the four runs!

Question: Do I get the same set of transcriptome representation between attempt 1 and attempt 2?

Note: Assuming that the probability of getting a very low abundant transcript is constant between runs, i would expect that the chance of observing these transcript in a smaller sampling size is less than in a higher sampling size

Predicted observation: In the second attempt after adding results I would expect that the transcriptome is overwhelmed only by transcripts of higher concentration in the sample, while I would expect to get more less abundant transcrips in the one time sequencing run with 50MilReads (attempt 1)

Thank you for your discussions!
go9kata is offline   Reply With Quote

3' tag, non-normalized library, transcriptome

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