The impact of quality filter for RNA-Seq

Gene
Pablo H C G de SáRommel T J Ramos

Abstract

With the emergence of large-scale sequencing platforms since 2005, there has been a great revolution regarding methods for decoding DNA sequences, which have also affected quantitative and qualitative gene expression analyses through the RNA-Sequencing technique. However, issues related to the amount of data required for the analyses have been considered because they affect the reliability of the experiments. Thus, RNA depletion during sample preparation may influence the results. Moreover, because data produced by these platforms show variations in quality, quality filters are often used to remove sequences likely to contain errors to increase the accuracy of the results. However, when reads of quality filters are removed, the expression profile in RNA-Seq experiments may be influenced. The present study aimed to analyze the impact of different quality filter values for Corynebacterium pseudotuberculosis (sequenced by SOLiD platform), Microcystis aeruginosa and Kineococcus radiotolerans (sequenced by Illumina platform) RNA-Seq data. Although up to 47.9% of the reads produced by the SOLiD technology were removed after the QV20 quality filter is applied, and 15.85% were removed from K. radiotolerans data set using the QV30 filte...Continue Reading

References

May 13, 2010·Briefings in Bioinformatics·Heng Li, Nils Homer
Jan 22, 2011·BMC Genomics·Vincent M Isabella, Virginia L Clark
Sep 8, 2011·Nature Reviews. Genetics·Jeffrey A Martin, Zhong Wang
Dec 14, 2011·Current Opinion in Biotechnology·Matthew B ScholzPatrick S G Chain
Apr 24, 2012·Nature Biotechnology·Nicholas J LomanMark J Pallen
May 30, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Anne Cybelle PintoVasco Azevedo
Oct 2, 2012·Current Opinion in Biotechnology·Kai-Oliver MutzFrank Stahl
Dec 29, 2012·BMC Genomics·Brian J HaasJonathan Livny
Dec 10, 2013·Bioinformatics·Yuwen LiuKevin P White
Jan 2, 2014·Frontiers in Genetics·Richard M LeggettRobert P Davey
Feb 28, 2014·Frontiers in Genetics·Stanley Kimbung MbandiAlan Christoffels

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