I have some RNAseq data mapped to the genome. for some of the genes, there is absolutely no reads mapped to them . however, when i do the PCR, they are expressing at a high level. clearly, there is something funky with the mapping.
Now, my question is: for the genes with very few reads, how can i distinguish between low expression and non-perfect mapping.
Now, my question is: for the genes with very few reads, how can i distinguish between low expression and non-perfect mapping.