Question: Comparison of a DGE result which has been aligned with Grch38 and SNP/INDeL information which has been obtained post alignment to Hg19
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gravatar for shubhrab
12 months ago by
shubhrab0
shubhrab0 wrote:

Hi everyone!

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.

rna-seq human snp genome • 263 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by shubhrab0

What exactly is the question you want to answer? Please add some details on exactly what you want to compare.

ADD REPLYlink written 12 months ago by ATpoint36k
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