FAIRE - computational pipeline
Overall structure of the FAIRE-seq pipeline. First, the pipeline allows the preprocessing of the reads by including different Fastx-Toolkit tools. Then, all steps involved in the alignment of the reads to the reference genome are included and automatized. From the processed alignment files, the identification of enriched regions is performed using MACS, CSAR and MOSAiCS. Mappability and GC content files are automatically computed as part of the pipeline. The output from the different peak callers is parsed to BED format and summit estimation, and filtering by each package score and by peak size is performed. To annotate the peaks according to their location, a parser of the annotation was developed storing the information in a MySQL database. This allows checking the overlap and/or the distance between the closest TSS and/or SC for each peak region. Finally a Gene Ontology term enrichment analysis and a motif analysis are performed.
About Me
Experience in applying scalable computational tools for the analysis of scientific data. Including analysis of data from next-generation sequencing technologies, simulation of different types of networks, modeling of biological/physicochemical processes, coupling geospatial data with biological data. Additional skills in web development, web scraping, and system administration. Familiarity using and deploying applications over high throughput and grid computing infrastructures e.g., University Clusters, Ohio Supercomputer Center, Open Science Grid, and The Worldwide LHC Computing Grid (WLCG). Experience working on big research teams and also with people from different backgrounds, supporting computing infrastructure, and debugging and producing patches on the fly. Eager learner interested in; analysis, design, and implementation of algorithms applied to any challenging problem; the Systems Biology field; and programming best practices.
$ 30 USD/hr
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