QuantSeq 3' mRNA-Seq

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Andrei Rozanski

May 25, 2020, 7:43:54 AM5/25/20
to RSEM Users

I would like to clarify if I can use RSEM to calclulate expression of 3' seq data (https://www.lexogen.com/quantseq-data-analysis/). 

From salmon's issues - https://github.com/COMBINE-lab/salmon/issues/449 I read:

... 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!

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