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
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
Thanks a lot
-- output of sessionInfo():
Sent via the guest posting facility at bioconductor.org.