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thelovelab / tximport

Transcript quantification import for modular pipelines
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Recomended count scaling method for DTU analysis #43

Closed kvittingseerup closed 4 years ago

kvittingseerup commented 4 years ago

When using tximport to import transcript level quantification with the end goal of performing DTU analysis which of the 4 count scaling methods would you recommend? (Asking since dtuScaledTPM was introduced after the Swimming downstream paper recommending "scaledTPM").

mikelove commented 4 years ago

scaledTPM or dtuScaledTPM are the ones that are appropriate for DTU, because the counts remain proportional to the TPMs within gene.

They are very similar. The latter keeps the scaled counts closer to the original counts however, which may be desirable.

kvittingseerup commented 4 years ago

Thanks