eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer’s disease mouse model

Hi

I am a beginner to prepare eQTL analysis using mouse model for alzheimer’s disease.

Is it possible to conduct eQTL analysis using ONLY brain RNA-seq data derived from 5XFAD or 3xtg mouse (The Jackson Laboratory)??

Thank you!

To perform an eQTL analysis you also need genotypic data 😀 If you have that, you can do it using RNA-seq data.

I have Bam file and vcf file. I got readcount matrix for rnaseq data. May you please tell me the steps to get eQTL