eQTL analysis in Galaxy

[muehlsch]

I am fairly new to NGS analysis and would like to perform a eQTL analysis in Galaxy. I have used the Galaxy NGS options extensively to run Tophat, Cufflinks, Cuffdiff, GATK, and VCF tools. Does Galaxy allow me to import expression data and perform a eQTL (e.g. Plink) analysis. My idea would be to convert the VCF file into a ped file ( I know VCFtools does this, but just not on Galaxy) and then use the GWAS tools in Galaxy to compare to expression.

What I have are RNA-seq data on humans.

Thanks so much for everyones help.

[suninsky]

I am not sure about galaxy, but there is a recent paper for eQTL using RNA-seq data, and the software can be found here

http://www.bios.unc.edu/~wsun/software/asSeq.htm