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Old 11-14-2012, 01:38 AM   #1
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Location: Oslo

Join Date: Nov 2012
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Default TSS analysis without biological replicates

I want to do a transcription start site analysis on a single-celled organism. The RNA-seq was done on two samples, one using the TAP enzyme to capture capped RNAs, the other being the control sample (thus without TAP). The difference between these two samples should give me potential TSSs.
The question is then how do I calculate the difference - I could try to subtract the coverage for the control case from the TAP+ case (or possibly use division instead). But how do I determine thresholds for what can be considered valid TSSs?
I have looked at the DESeq and edgeR packages in Bioconductor, but it is clear that I would need multiple biological replicates to use those (which I do not have, I have only the two TAP+ and control samples).
Thank you for any help and feedback!

ralfne is offline   Reply With Quote

expression levels, rna-seq, transcription start site

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