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Background: When estimating relative transcript abundances by quantitative real-time PCR (Q-PCR) we found that the results can vary dramatically depending on the method chosen for data analysis.

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The ever-increasing number of genome sequencing and resequencing projects is a central source of insights into the ecology and evolution of non-model organisms. An important aspect of genomics is the elucidation of sex determination systems and identifying genes on sex chromosomes. This not only helps reveal mechanisms behind sex determination in the species under study, but their characteristics make sex chromosomes a unique tool for studying the mechanisms and effects of recombination and genomic rearrangements and how they affect adaption and selection. Despite this, many sequencing projects omit such investigations. Here, we apply a simple method using sequencing coverage statistics to identify scaffolds belonging to the sex chromosomes of minke whale, and show how the sex chromosome system can be determined using coverage statistics alone.Using publicly available data, we identify the previously unknown sex of an Antarctic minke whale as female. We further investigate public sequence data from the different species and sub-species of minke whale, and classify genomic scaffolds from a published minke whale assembly as X or Y chromosomal sequences. Our findings are consistent with previous results that identified a handful of scaffolds as sex chromosomal, but we are able to identify a much larger set of scaffolds, likely to represent close to the complete sex chromosomal sequences for the minke whale.Sequence coverage statistics provides a readily available tool for investigating the sex determination system and locate genes on sex chromosomes. This analysis is straightforward and can often be performed with existing resources.