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

Source Code for Biology and Medicine

Jun Sese²  Akiko Izawa¹ 

[1] Department of Computer Science, Ochanomizu University, Tokyo, Japan;Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan

关键词: Comparative transcriptomics;    Comparative genomics;    ChIP-seq;    RNA-seq;    Next-generation sequencers;   

Others  :  805810
DOI  :  10.1186/1751-0473-8-6

 received in 2012-01-17, accepted in 2013-02-19,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Izawa and Sese; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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