A SIROCCO pipeline has been developed for analysing the results of high throughput sequencing experiments. It is currently used most often for Illumina reads but can be used to process 454 reads as well.
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Silencing RNAs: organisers and coordinators of complexity in eukaryotic organisms
SIROCCO Tools
Here is a list of tools which can be used to process data for silencing RNA. Unsure how to proceed? Try our getting started guide.
The Sirocco Pipeline – A Bioinformatics Service for SIROCCO Members
WMD3 – Web MicroRNA Designer
WMD (Web MicroRNA Designer) is a web-tool for the automated design of artificial microRNAs. Version 3 was released in July 2009.
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baySeq Differential Analysis Tool
baySeq is a package for calculating Differential Expression in Solexa-type, or count, data for the R Project For Statistical Computing. It was previously available on these pages but is now part of Bioconductor. For more information please see the Bioconductor website.
For details on the methods being used, consult Hardcastle et al. (2009) Empirical Bayesian methods for estimating differential expression in count data.
Arabidopsis thaliana – Tiling Array Express (At-TAX)
At-TAX is a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Tiling array hybridization intensities, probe set definitions for Arabidopsis genes and segmentations into exonic and background regions are visualized in a genome browser. Visualizations of gene expression and cross-platform comparisons are available through tileViz.
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SHORE – Short Read Sequencing
SHORE is a tool for the analysis of Illumina Genome Analyzer expression data, including both mRNA sequencing (mRNA-seq) and small RNA sequencing (sRNA-seq). It includes preprocessing and quality filtering of Illumina GA reads, mapping of reads against a reference genome, splice site detection for mRNA-seq as well as quantitative expression analysis and visualization.
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