NGS-Trex: Next Generation Sequencing Transcriptome profile explorer

Abstract

BackgroundNext-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics skills and computational resources well beyond the possibilities of many "wet biology" laboratories. Moreover, most of projects only require few sequencing cycles and standard tools or workflows to carry out suitable analyses for the identification and annotation of genes, transcripts and splice variants found in the biological samples under investigation. These projects can take benefits from the availability of easy to use systems to automatically analyse sequences and to mine data without the preventive need of strong bioinformatics background and hardware infrastructure.ResultsTo address this issue we developed an automatic system targeted to the analysis of NGS data obtained from large-scale transcriptome studies. This system, we named NGS-Trex (NGS Transcriptome profile explorer) is available through a simple web interface http://www.ngs-trex.org and allows the user to upload raw sequences and easily obtain an accurate characterization of the transcriptome profile after the setting of few parameters required to tune the analysis procedure. The system is also able to assess differential expression at both gene and transcript level (i.e. splicing isoforms) by comparing the expression profile of different samples.By using simple query forms the user can obtain list of genes, transcripts, splice sites ranked and filtered according to several criteria. Data can be viewed as tables, text files or through a simple genome browser which helps the visual inspection of the data.ConclusionsNGS-Trex is a simple tool for RNA-Seq data analysis mainly targeted to "wet biology" researchers with limited bioinformatics skills. It offers simple data mining tools to explore transcriptome profiles of samples investigated taking advantage of NGS technologies.

The RNA‐binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs

“…After 2 cycles of selections, phagemid DNA was extracted from the eluted phage pool, and ORF inserts were sequenced on an Illumina platform. We analyzed ∼100,000 reads from each selected library with the NGS-Trex system (37, 39). Table 1 shows a summary of the sequencing analysis.…”

“…We then performed a fold enrichment analysis to assess those genes whose ORFs were enriched after selection (37, 39). This analysis was carried out by comparing sequencing outputs of each selection with the NS library, the latter serving as a reference.…”

“…Sequences were processed with the NGS Transcriptome Profile Explorer (NGS-Trex) system ( https://www.ngs-trex.disit.unipmn.it/Trex/cms/ ) as previously described (36, 39). Briefly, sequences were mapped onto the human genome (U.S. National Center for Biotechnology Information Build 36) using genomic mapping (GMAP) software, and matching sequences were compared with annotated genes.…”

Bioinformatics in Italy: BITS2012, the ninth annual meeting of the Italian Society of Bioinformatics

“…The article "NGS Trex - Next Generation Sequencing Transcriptome profile explorer" by Boria et al [9] describes NGS Trex, a new pipeline system that analyses RNA-seq data: the system automates the process of investigating raw data by mapping reads to reference genomes, and also analyzes differential expression of genes and splice variants.…”

Plant-Microbe Interaction: Transcriptional Response of <em>Bacillus Mycoides</em> to Potato Root Exudates

“…The expression of the IclR transcriptional regulator, which is related to multidrug resistance and the degradation of aromatic compounds in soil bacteria, is upregulated. The IclR deletion strain of rhizobacteria Klebsiella Copyright © 2018 Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License July 2018 | 137 | e57606 | Page 7 of 7 pneumoniae has decreased the mineral phosphate solubilization, compared with the wild-type strain 19 . Several genes related to amino acids metabolism and synthesis are stimulated, while genes involved in sugar transport including a cellobiose PTS transporter are downregulated.…”