I am quite new at analysing NGS data, but I am trying to set up a pipeline for my lab. We have performed single end sequencing using Ion Torrent Proton to analyse differential gene expression (through QuantSeq 3' mRNA-seq). I am testing alignment using the Hisat2 aligner, however I am not sure whether I need to use the parameter --no-templatelen-adjustment. I read the manual and paper describing the aligner, but it is not quite clear for me what this parameter does exactly. Can anyone help?
Thank you in advance.