Brief. Bioinformatics - Comparison of software packages for detecting differential expression in RNA-seq studies.

Tópicos

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Resumo

RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a number of data analysis methods and pipelines have already been developed for this task. Currently, however, there is no clear consensus about the best practices yet, which makes the choice of an appropriate method a daunting task especially for a basic user without a strong statistical or computational background. To assist the choice, we perform here a systematic comparison of eight widely used software packages and pipelines for detecting differential expression between sample groups in a practical research setting and provide general guidelines for choosing a robust pipeline. In general, our results demonstrate how the data analysis tool utilized can markedly affect the outcome of the data analysis, highlighting the importance of this choice.

Resumo Limpo

rnasequenc rnaseq rapid becom popular tool character transcriptom fundament research problem mani rnaseq studi identif reliabl molecular marker show differenti express distinct sampl group togeth grow popular rnaseq number data analysi method pipelin alreadi develop task current howev clear consensus best practic yet make choic appropri method daunt task especi basic user without strong statist comput background assist choic perform systemat comparison eight wide use softwar packag pipelin detect differenti express sampl group practic research set provid general guidelin choos robust pipelin general result demonstr data analysi tool util can mark affect outcom data analysi highlight import choic

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