I have a mutations which have been annotated (obtained from Annovar) of .vcf files which was obtained after alignment to Hg19.
I have downloaded RNA seq data from Allen Brain Atlas which have been calculated using Grch38 genome Hence, I have the normalized expression values of genes which I am interested in.
So, I have mutation information in the genes of interest and also their FPKM value. My question is can there be a comparison between the exome(SNP/INDel) data and transcriptome data (Allen Brain atlas) if they are from two different versions of human genome.
Also, any ideas/articles about how I can compare the exome and transcriptome data is helpful.
PS: I want to look at the expression levels of genes of my interest( these genes of interest have been shortlisted from the .vcf file according to the phenotype of interest.)
--Thanks in advance.