Expression quantification

[stsergbg]

Hi,

I have a question regarding the options for salmon/sailfish 3'UTR quantification. Should sailfish/salmon be used with the default options (provided that the data is mostly TCGA-like) or do you have any insights on the parameters that usually work best, e.g. (salmon) using --validateMappings or decoy-aware transcriptome? I haven't tried sailfish but I'm going to try it too, so if there are some options I'd better try changing, that would be helpful to know. I just couldn't find information on that in the paper.

Sergei