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An automatic workflow for microRNASeq analysis

AutorNúñez-Torres, Rocío; Andrés-León, Eduardo; Rojas, A. M.
Fecha de publicaciónsep-2014
CitaciónXII Symposium on Bioinformatics (2014)
ResumenIn the past few years, the study of microRNAs (miRNAs) attracted attention due to their important role in post-trans-criptional fine tuning regulation of gene expression. Altered expression of miRNA has been associated to several pathological conditions such as cancer or infectious diseases. The development of Next Generation Sequencing technologies has enabled novel approaches for the expression studies of miRNAs using Small RNASeq technology. Due to crucial differences among standard RNASeq and Small RNASeq analyses, we have developed a miRNASeq analysis workflow, which automatically performs several analysis processes using state-of-art software. Briefly, our process includes: (a) Quality analysis of the reads (by FASTQ) (b) Adapter removal using Cutadapt [1] or Reaper [2]. If the adapter information is not available a computational prediction of the adapter sequence can be performed using Minion [2] (c) Alignment to the reference genome (indexing is included within the pipeline) (by Bowtie1/2 [3-4]) (d) Read quantification by desired feature (premiRNA, mature miRNA...) using Htseq-Count [5] (e) Quality analysis to determine the correlation among replicates using graphical approaches, such as PCA, MDS or hierarchical clustering (f) Differential Expression Analysis (DEA) using EdgeR [6] and/or NOISeq [7]. Our pipeline process standard sequencing files (fastq format) performing several and parallelized analysis resulting in a results file (tsv format) with DEA features for each experimental condition evaluated and an additional quality report file. The pipeline presented here has been successfully applied to analyze miRNASeq data obtained from a time course experiment performed in the MCF7 cell line in hypoxic conditions [8] presenting analogous results. This workflow has been established by the Computational Biology and Bioinformatics group at IBIS to perform their miRNASeq analyses.
DescripciónTrabajo presentado en el XII Symposium on Bioinformatics (XII Jornadas de Bioinformática), celebrado en Sevilla del 21 al 24 de septiembre de 2014.
Aparece en las colecciones: (IBIS) Comunicaciones congresos
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