I'm starting to learn RNA seq analysis. I have a paired-end, stranded RNA dataset sequenced with Illumina TruSeq; it includes RNA from a human cell line in multiple conditions. I've used Galaxy to do differential mRNA expression analysis successfully.
The lab I'm working with is now curious about differential expression of little-studied group of small RNAs called tRNA-derived fragments, or tRFs for short. tRFs are ~20 nucleotides in length and there are ~23,000 known human tRFs, and these sequences are listed in an online database (https://cm.jefferson.edu/MINTbase/).
Before I invest time in trying to learn to do this analysis, I'm trying to figure out whether these small RNAs would even be present in the raw data I have.
Are small RNAs like this typically removed during the processing of the biological sample? or can I expect all the different types of RNA to be present in the raw data?