Pre-pseudoalignment preprocessing

Question

[Nicholas]

Salmon makes a number of modifications to its output in response to different biases it detects. Is it bad, then to remove certain classes of reads by using another aligner and removing, say, non coding sequences before using salmon? If that isn't okay, is there an alternative way to do that afterwards?

Answer 1

[ATpoint]

I do not see the point in doing such a filtering. If later you want to focus on certain gene biotypes then filter the count table for it, but suggested upstream processing is non-standard and laborious, while a subset on a count table literally takes seconds.