This could be a easy solution but just wanted to get your opinion on this. We have 10 different small RNA samples sequenced for arabidopsis. They are varied in read numbers from 10 million to 30 million . We wanted to look at reads mapping to 5' end of a gene. I used that gene as reference and mapped all the reads and got read counts mapping to it.
So to get relative expression, can i use simple normalization using total reads as my reference is only one gene or should i use proper techniques such as TPM or TMM ?