RNA-Seq uses the high-throughput sequencing technology to identify and quantify transcriptome at an unprecedented high resolution and low cost. However, RNA-Seq reads are usually not uniformly distributed and biases in RNA-Seq data post great challenges in many applications including transcriptome assembly and the expression level estimation of genes or isoforms. Much effort has been made in the literature to calibrate the expression level estimation from biased RNA-Seq data, but the effect of biases on transcriptome assembly remains largely unexplored.