title: PIPE-chipSAD:A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes.
abstract: PIPE-chipSADis a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithmchipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure,align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions. Finally, the pipeline includesanno-chipSADa method to annotate the detected transcripts in comparison to the genome annotation. Overall, our pipeline allows transcriptional profile analysis of both coding and non-coding portions of the chromosome in a single framework. Importantly, due to its versatile characteristics, it will be of wide applicability to analyse, not only microarray signals, but also data from other high throughput technologies such as RNA-sequencing. The currentPIPE-chipSADimplementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD.
authors.affiliation: GSK Vaccines Srl Siena, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Bottini
authors.affiliation: GSK Vaccines Srl Siena, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Del Tordello
authors.affiliation: GSK Vaccines Srl Siena, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Fagnocchi
authors.affiliation: Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Donati
authors.affiliation: GSK Vaccines Srl Siena, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Muzzi
keywords: code:python; high density arrays; microarrays; tiling arrays; transcriptomes