eQTL Detector; an automated pipeline for eQTL mapping and downstream analysis
Access to both DNA and RNA genotyping technologies have opened a new paradigm in the mapping of complex characters, these are based on the evaluation of the interaction of the genotype and other variables such as methylations, proteins or levels of gene expression, in relation to this last variable,...
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| Tipo de recurso: | tesis de maestría |
| Fecha de publicación: | 2020 |
| País: | España |
| Institución: | Universitat Oberta de Catalunya (UOC) |
| Repositorio: | O2, repositorio institucional de la UOC |
| OAI Identifier: | oai:openaccess.uoc.edu:10609/121606 |
| Acceso en línea: | http://hdl.handle.net/10609/121606 |
| Access Level: | acceso abierto |
| Palabra clave: | eQTL Docker pipeline GWAS Bioinformatics -- TFM Bioinformàtica -- TFM Bioinformática -- TFM |
| Sumario: | Access to both DNA and RNA genotyping technologies have opened a new paradigm in the mapping of complex characters, these are based on the evaluation of the interaction of the genotype and other variables such as methylations, proteins or levels of gene expression, in relation to this last variable, expression QTLs (eQTL) try to determine the level of expression of each gene based on each of the variants of the organisms in whole genome basis, the variants can be close to the gene of interest, in a range of 1Mb, _cis_-eQTL, or distant in a range greater than 1 Mb, called _trans_-eQTL. The amount of data necessary to perform this type of studies requires the use of tools that are easy to implement and that guarantee reproducible results. The use of containers in bioinformatics has been one of the solutions to this problem, then Docker is one of the most widely used. On the other hand, different tools that can map eQTL have existed for more than a decade, but there is one that stands out above the others, QTLtools, an application easy to implement, efficient in the use of hardware and also contains different modules that goes from quality control of samples to the co-localization of eQTL with GWAS hits. In this work we present eQTL_Detector, an automated pipeline that uses the QTLtools modules as a base and integrates them into a container that generates a report using the statistical software R and R Markdown functionalities for the creation of the report. In addition, in this work we describes each of the steps of this pipeline describing the inputs and outputs for each step together with their statistical foundations. |
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