Hi I have two questions..
1. I wanted to compare the SNPs variation due to transcription. So, I called SNPs from RNA-Seq of 321 samples of two different tissues. Please guide me which software I need to use and which pipeline needs to follow to know the variations due to transcription compare the SNPs of DNA ( I have the DNA-SNPs data from the same 321 samples).
2. How I can see the difference/explain the differences among GAWS-SNP target traits are common in two tissues. For example, I used two tissues and I found some target traits are commonly targeted by GWAS (SNP+expression+phenotype) in two tissues.
1-
I suggest you try using this tool. It finds SNPs between two sequences of the same sample. httpss://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851604/
2- you could annotate these SNPs and highlight certain outcomes based on the effect of an amino acid change (missense/ nonsense or polar/nonpolar). you can use SNPEFF for this kind of analysis after calling SNPs
Dear Balig Panossian ,
Many thanks for your kind reply and suggestions!
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