The effect of various filters on fast RNA-seq quantification

Question

[Pappu]

I am wondering what is the effect of following filters before using fast quantifiers like salmon/kallisto:

1. Adapter trimming
2. Size selection
3. Quality filtering

[Kevin Blighe]

The investigator in you should immediately have the impetus to go and check yourself.

[h.mon]

Instead of wonder, search. If not present on the original Salmon and kallisto papers, there may be a manuscript with an independent comparison. As Salmon and kallisto are somewhat recent, you may not find manuscript including them in the comparison, then you may try and perform the test yourself.