Pipeline to analyse small RNAseq and tRNAs? I am a newbie in this world (just finished my master's on bioinformatics. As a practice, a researcher gave me 4 fastq files from a small RNAseq experiment, to see if I am able to reproduce their results but with an updated pipeline and tools (they used bowtie in 2014). 
I used fastqc for the quality check and I removed the adapters properly. 

My first intention was to use Salmon for pseudo-align them, but after do some reading it seems not to be a good idea for such small RNAs. 

Can anyone provide me with some light on this? Which alignment tool use and which parameters, and etc. Ideally a proper protocol/pipeline would be amazing. 

Thank you in advance...

PD: I was thinking to use the HISAT2 with the full genome (or the pre-builded index from HISAT2 website). 

Kind regards, 
and thank you in advance!
I have heard that the Small RNA Workbench from UEA can be an easy solution for a full small RNA pipeline.  It is java based, has a GUI, and is supposed to be easy to install and run.  I am not an expert in small RNA analysis, but I think this pipeline will certainly given you an idea about the steps needed for a small RNA analysis, it has been put together by experts.