quantify tRNA-derived fragments on RNA-seq data

Question

[lkianmehr]

I have some questions:

1- can I seek for tRNA-derived fragments or generally small coding and non-coding RNA on RNA-seq data?

2- if so, is Salmon useful for this purpose?

thank you

[ATpoint]

I doubt that you will get reliable information from that in standard RNA-seq. The polyA-enrichment that is routinely done does not capture these transcripts since they are not polyadenylated.