[BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments

[Gilgi [guest]]

Hello,
I wanted to ask whether it is possible to use DESeq for the analysis of translation efficiency in polysome profiling or ribsome profiling.
In polysome profiling - polysomes are isolated (e.g. by sucrose gradients), and mRNA that were associated with the polysomes are then isolated and sequenced.
In ribosome profiling, mRNA fragments that are protected by the ribosome are sequenced.
When such experiments are conducted in parallel to total RNA-seq, one can ask questions regarding the translation efficiency.
For example: if we have 4 samples: ribosome sequencing (without treatment), total sequencing (without treatment), sequencing (with treatment), total sequencing (with treatment), one can ask how does the treatment affects the protein synthesis rate (which is the ratio ribosome/total).
I wanted to ask whether it is possible to define such a model in DESeq for such analysis, in order to answer how is this ratio affected by the treatment.
Thanks a lot


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