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. 2011 Mar 17;12:75. doi: 10.1186/1471-2105-12-75

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Copyright © 2011 Kim et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Workflow of AnyExpress. An outline of data flow is depicted with input, output, and intermediate files. Core processes in AnyExpress are drawn as blue rectangles. Pre-processing is represented by yellow rectangles. ALIGN is an external process (pink trapezoid) that runs via software such as Bowtie or RMAP. The standard input to AnyExpress is a Browser Extensible Data (BED) file or a tab-delimited multi-column file. The output is a target-by-sample combined file. A gene-by-sample is used in the final output of this figure, but the user can choose his/her own target (e.g., 'RefGene isoform' or 'Ensembl gene') by running anyexpress Build.