I am working on a RNA-seq analysis of mice. My workflow is as follows.
- quality filtering of reads
- using bowtie2-build to index my reference genome
- performing rsem-prepare-reference with gtf file for mouse genome (Mus_musculus.GRCm39.dna_sm.toplevel.fa)
- aliging NGS reads to reference genome using bowtie2.
- using rsem-calculate-expression for obtaining expected frequencies of genes.
I have been reading about Trinity. It suggests evaluation of the quality of transcriptome assembly. I am not using trinity, I am using rsem. With rsem and the reference genome, do I still need to perform the quality of assembly at any point Do I need to evaluate the quality of assembly at any point? If the answer is yes, can you explain? if answer is no, can you explain?
Please, excuse me if I am asking you an obvious question. I have zero experience on this.