Hello all
Im scoping out an analysis pipeline for a large eQTL experiment we are planning. Weve already done a pilot experiment on 30 samples (~100M PE reads) and have been playing with DEseq and Cuffdiff to try and detect differential expression by genotype. However neither of these programs are suited to conducting eQTL analysis, since both are geared for pairwise comparison (versus quantitative fit on allele copy), and Cuffdiff especially takes a LONG time to run (waiting days per comparison isnt really feasible when we want to analyse in conjunction with 1M+ SNP!).
SO, are people here using RNAseq data for eQTL analysis and if so how are you approaching this? Given the number of microarray eQTL studies I was surprised to see how little has been published using RNAseq data. Ultimately Id like to derive expression levels for each gene (and isoform thereof) and use this in conjunction with the likes of Plink or some other computationally efficient mapping software. I have considered using the counts (from bedtools or HTseq) or FPKMs out of cufflinks, but again interested to hear what others are doing...
Thanks in advance
Matt
Im scoping out an analysis pipeline for a large eQTL experiment we are planning. Weve already done a pilot experiment on 30 samples (~100M PE reads) and have been playing with DEseq and Cuffdiff to try and detect differential expression by genotype. However neither of these programs are suited to conducting eQTL analysis, since both are geared for pairwise comparison (versus quantitative fit on allele copy), and Cuffdiff especially takes a LONG time to run (waiting days per comparison isnt really feasible when we want to analyse in conjunction with 1M+ SNP!).
SO, are people here using RNAseq data for eQTL analysis and if so how are you approaching this? Given the number of microarray eQTL studies I was surprised to see how little has been published using RNAseq data. Ultimately Id like to derive expression levels for each gene (and isoform thereof) and use this in conjunction with the likes of Plink or some other computationally efficient mapping software. I have considered using the counts (from bedtools or HTseq) or FPKMs out of cufflinks, but again interested to hear what others are doing...
Thanks in advance
Matt