I'm new to RNAseq, so I'm confused with a couple of terms.
As I understand, raw counts are generated by sequence aligning. Is it right?
And then, expected counts are generated by running RSEM with raw counts, right?
This is to correct sequence reads mapped to more than one spot or alternatively spliced variants. Is this right?
Then, expected counts are not normalized by length of genes. Did I understand correct?
I guess, this is pretty simple things, but I'm still a little confused when someone asks me..-.-v
Please correct, if I have misunderstanding.
Thanks in advance. MH