Hello everyone!
I have a question regarding the processing pipeline of tRFs in rat samples.
I have three groups control and two stressed conditions (unfortunately too little samples each group)
I am interested in doing DGE analysis and I need to take into account full length tRNAs and tRFs as well. So what I did I used bed file from tRNAscan-SE and generated a custom annotation file (gtf) then I combined it with the last annotation of rattus norvegicus. I trimmed adapters with TrimGalore and then I used STAR for the alignment. I generated unmapped reads files and then I analyze it with MINTmap tool (deterministic and exhaustive search of tRF in fastq files). I wanted to exclude ambiguous reads between tRNA and tRF so I did mapping of raw reads first. Then I did featureCounts on aligned reads and combined an output from MINTmap base and tried to make DGE analysis. How accurate such analysis would be and am I allowed to combine counts from the usual alignment with the output of this tool? What is the best way to analyze such data?
How to normalize the expression in that case?
