Abstract
Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications (e.g. uridylation, adenylation), 5′-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface.Availability and implementation: Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira.Contact: aje@ebi.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Small RNA sequencing data are among the most straightforward types of NGS data to analyse
Plain Counts refers to the quantification of the miRNA molecules that are expressed in any form in each of the input samples
The input sequences are mapped against miRBase using BLASTn (Boratyn et al, 2013) allowing up to two mismatches for each sequence
Summary
Small RNA sequencing data are among the most straightforward types of NGS data to analyse. In recent years, it has been reported that many miRNAs go through post-transcriptional alterations that modify their 30 end, mainly via mono/poly-Uridylation (Heo et al, 2009, 2012) or polyAdenylation (Shanfa et al, 2009) Such modifications are believed to impart significant functional changes to the miRNA. D.M.Vitsios and A.J.Enright miRNA is analysed to detect bases in the miRNA sequence that could not possibly have derived from the precursor it aligns to These unalignable nucleotides are likely either: (i) base-calling errors, (ii) single nucleotide polymorphisms (SNPs), (iii) ADAR edits or (iv) post-transcriptional miRNA modifications (e.g. via TUTases). In order to study this diverse pool of possible miRNA post-transcriptional modifications, we have developed Chimira This is a cohesive platform for the processing and analysis of small RNA NGS data allowing simultaneous detection of 30, 50 and internal miRNA modifications. The system provides a simple interface for computationally determining likely 30 sequencing adapters in case the user does not have this information
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