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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4.7 years ago

shubhrab • 0

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 SNP human genome • 610 views

ADD COMMENT • link 4.7 years ago by shubhrab • 0

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

ADD REPLY • link 4.7 years ago by ATpoint 82k

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