Driver-ASE testing dataset

Published: 3 September 2021| Version 5 | DOI: 10.17632/8x3y5swppw.5
Contributor:
zhongshan cheng

Description

(1) This 'Database.zip' is required by Driver-ASE, which is a software to search for potential driver mutations located in different regulatory regions by associating mutations with gene-level ASE. Due to the large size of the impute2 and shapeit reference datasets, we make it freely available at the following shared link via https://mega.nz: https://mega.nz/file/p1R0iZjB#SBHjUncZf4qomuBkfw2r8GnquDK1wgE0DAw20IEsRcc Alternatively, we uploaded a partial data of 'Database.zip' here, which doesn't have impute2 and shapeit reference datasets and is named as ''PartialDatabase4DriverASE.tar.gz'. Users can download the original impute2 and shapeit datasets from the following links and put them into the uncompressed directory of 'Database' for running our package Driver-ASE. #Download 1000 Genome Project reference haplotype files; #https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html wget https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.tgz wget https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3_chrX.tgz #Download shapeit2 phased 1000 Genome Project reference files; #https://mathgen.stats.ox.ac.uk/impute/data_download_1000G_phase1_integrated_SHAPEIT2_16-06-14.html wget https://mathgen.stats.ox.ac.uk/impute/ALL.integrated_phase1_S#HAPEIT_16-06-14.nomono.tgz (2) The 'Pipeline2MapMuts2DiffRegulatoryRegions.zip' contains perl scripts for mapping mutations to different regulatory regions and prepare mutation annotation data for associating mutations with gene-level ASE, which is detailed in the github of Driver-ASE (https://github.com/MichealRollins-Green/Driver-ASE). Note: please run the shell script 'Run_Pipeline.sh' under the directory contain it in Linux system! The final results would be in the directory 'final_outputdir'.

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Categories

Cancer, DNA Mutation

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