Benchmarking of RNA-seq data processing pipelines using whole transcriptome qPCR expression data

Jan Hellemans1, Jo Vandesompele1,2, Pieter Mestdagh1,2
1Biogazelle, Belgium; 
2CMGG, UGent, Belgium

RNA sequencing is becoming increasingly popular to perform transcriptome wide gene expression analyses. The recently published SEQC study assessed the performance and key characteristics of RNA-seq by sequencing the MAQC samples to very deep coverage. We have extended this study by detailed comparison of the results generated by different data processing pipelines against those obtained by transcriptome wide qPCR measurements. The relative performance and differences between 4 pipelines (Sailfish, tophat-HTseq, star-HTseq and tophat-cufflinks) as well as their concordance to qPCR data will be presented.

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