The ‘mut_ase_auto’ directory contains the ‘mutation x regulatory-feature’ MATLAB matrix.Ĭomputational Resources. (B) The raw association p-values (assoc_P_all.tab), FDR values (fdr_all.tab), mutation enrichment p-values for each feature with each gene (fm_all.tab), and information for samples harboring these regulatory mutations (mut_all.tab) are output into the ‘hits’ directory. The directory ‘hits’ will contain all ASE-Mut association results as shown in the lower panel. The bed files of putative driver mutations can be visualized with the UCSC or alternate genome browsers (hg19). For example, the upper box shows an association between RALGPS1 and mutations within 10kb of its TSS and gene body that is found using the demo data of 46 BRCA samples.
After running the pipeline the ‘Driver_beds’ directory will contain one text file of all associations FDR<0.2 (driver_top_fdr0.2), and a bed file for each association between a mutated cis-regulatory element and gene-level ASE. (A) The ASE-Mutation associations are saved in the ‘BRCA’ directory that includes 3 subdirectories: ‘Driver_Beds’, ‘hits’, and ‘mut_ase_auto’. The directory tree of the final ASE-Mutation results See ‘ potential problem 6’ to resolve issues in running the MATLAB executable file in a local Linux system. Note: MATLAB runtime version 90 must be installed in a local Linux system or online cluster, the installation of which should be completed when running the shell script for the installation of Driver-ASE in the system via conda. M1_Import_ASE_and_Mutation_data BRCA '.∗' 0.2 #Note: the regular expression ‘.∗’' will match all 18
MATLAB executable will generate the same results as thatĮxecuting in MATLAB shown in the previous section of #When running the following command in a Linux terminal, the #This will print help information for the MATLAB executable #Parameters required by the executable file. Driver_ASE/Driver_ASE_MatLab/Driver_ASE_MatLab_Lib/Driver_A Shapeit2 phased 1000 Genome Project reference filesġ000 Genome Project reference haplotype files
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