AUTHOR=Bottini Silvia , Del Tordello Elena , Fagnocchi Luca , Donati Claudio , Muzzi Alessandro 

TITLE=PIPE-chipSAD: A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=3

YEAR=2016

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2016.00082

DOI=10.3389/fmolb.2016.00082

ISSN=2296-889X

ABSTRACT=<p><italic>PIPE-chipSAD</italic> is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm <italic>chipSAD</italic>, 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, <italic>align-chipSAD</italic>, 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 includes <italic>anno-chipSAD</italic> a 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 current <italic>PIPE-chipSAD</italic> implementation is written in Python programming language and is freely available at <ext-link ext-link-type="uri" xlink:href="https://github.com/silviamicroarray/chipSAD" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/silviamicroarray/chipSAD</ext-link>.</p>