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

Question

[swordbreadjj]

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!

[Arup Ghosh]

But, is not eQTL is the association of expression and genotype data?

[erdiazval]

You can use RNA-seq data to mine genetic markers (SNPs & indels) and also to generate expression profiles and perform an eQTL analysis. However, if your are using exon/CDS data, I think your are going to have a very small number of markers in comparison to that you could obtain from whole genome sequencing, whole exome or tGBS. In our lab we have a simple pipeline, we generate expression profiles via RNA-seq (10 million reads p library) and from the same individuals, we generate markers via tGBs (targeted genotyping by sequencing). This methods is relatively cheap (17k RNA-seq + 9 k tGBS) for ~96 individuals. But, if the mice your are testing for regulatory divergence have enough genetic differentiation, I think that RNA-seq-derived markers could be enough to build a linkage map. Happy bioinformatics!

Answer 1

[Selenocysteine]

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

Answer 2

[Nai]

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

[ahmedakhokhar]

http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/