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Old 02-03-2014, 12:00 PM   #1
ahodgins
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Location: New Haven, CT

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Default Tag-Seq vs RNA-Seq

Hi all,

Does anyone know of any papers directly comparing RNA-Seq to Tag-Seq results? (Ideally, DpnII digital expression count data in yeast, but I'd take what I could get.)

The situation: We have some old data using DpnII tag profiling to compare our homemade microarrays with Illumina digital gene expression counts. Its a rich dataset using two different priming methods to compare across platforms (microarrays vs digital Tag-Seq). Now, I have an additional RNA-seq dataset prepared with random fragmentation, not restriction endonuclease-generated tags. I'd love to be able to use the work we've already done to robustly compare my new RNA-Seq data to the same microarrays, but I'm aware that the Tag-Seq results are not directly comparable to the RNA-Seq results. What I'm wondering is if I can reasonably estimate the relationship by counting DpnII cut sites and scaling RNA-Seq counts by gene length or whether there are some further effects I'm missing.

Thanks for any insight you can offer!

Andrea
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Old 04-04-2020, 01:55 PM   #2
DPresto
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Default

Hi Andrea,

Apologies for resurrecting such an old thread, but I wanted to know if you ever got a satisfactory answer to this question, as I have the same one.

Best,

-Devin
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