... Correct; as far as we are aware, there is no way to disable the built-in length-dependent assumptions of RSEM. One could use the
--estimate-rspd flag to allow learning of a non-uniform read distribution (the equivalent of
--posBias in salmon), though it's unclear / unlikely if this would be as effective as fully disabling the length correction for this type of tagged-end data. If you have any good empirical assessment mechanism for QuantSeq data, and a chance to test out these different salmon options, we'd be happy to get feedback and discuss details further! ...
However, its not clear to me if --estimate-rspd makes RSEM usage possible/applicable in this case or not.
Thanks for all the help!