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Background  The whole-genome sequences of many non-model organisms have recently been determined. Using these genome sequences, next-generation sequencing based experiments such as RNA-seq and ChIP-seq have been performed and comparisons of the experiments between related species have provided new knowledge about evolution and biological processes. Although these comparisons require transformation of the genome coordinates of the reads between the species, current software tools are not suitable to convert the massive numbers of reads to the corresponding coordinates of other species’ genomes.    Results  Here, we introduce a set of programs, called REad COordinate Transformer (RECOT), created to transform the coordinates of short reads obtained from the genome of a query species being studied to that of a comparison target species after aligning the query and target gene/genome sequences. RECOT generates output in SAM format that can be viewed using recent genome browsers capable of displaying next-generation sequencing data.    Conclusions  We demonstrate the usefulness of RECOT in comparing ChIP-seq results between two closely-related fruit flies. The results indicate position changes of a transcription factor binding site caused sequence polymorphisms at the binding site.

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics