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!