I am a student in Master and i don't understand a result of rna-seq :
We have performed four alignments : Rna-seq from "PGF" cell on the genome of this cell + genome of "COX" cell Rna-seq from COX" cell on the genome of this cell + genome of "PGF" cell
Actually we have not used the whole genome map but only the short arm of Chr6 on which there is the CMH. As expected we get more reads aligned with the genome corresponding to the cell on which the rna-seq is performed but i don't understand why is the percentage of mismatch higher for rna-seq of PGF on PGF genome than for rna-seq of PGF on COX genome (The same thing happen for COX rna-seq result -> Higher mismatch when aligned with COX genome than with PGF genome).
How is that possible ? Does that mean that when we align with the good genome, we have more RNA actually corresponding to mRNA (spliced mRNA) and when we don't align with the good genome, we have more RNA corresponding to non-coding RNA ?