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shunliubio / eTAM-seq_workflow

A workflow for eTAM-seq data processing.
GNU General Public License v3.0
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eTAM-Seq without ivt ? #8

Open Maschi88 opened 4 months ago

Maschi88 commented 4 months ago

Hello,

I have another question concerning this pipeline. The m6A accessibility and level are calculated using in vitro samples : do you think it is possible to estimate the m6A accessibility in a mutant (e.g. where methylation is more or less deposited on RNA) without ivt calibration ? Or ivt is highly recommanded for doing eTAM-Seq ?

I would like to raise this point as the variables in the R library are literally "FTO" and "IVT" and then rather difficult to adapt to any other experiments in the field.

Thanks for reading, Best

shunliubio commented 3 months ago

We need external controls (e.g., FTO or IVT) to estimate m6A accessibility and methylation. Both FTO and IVT serve as (nearly) modification-free transcriptome. As IVT is an in vitro transcription method, FTO samples can give us a more consistent source of reference transcriptome than IVT samples. They can complement each other.