A meQTL/eQTL detection method based on Gradient Boost Tree model by using recombination rate and HiC signal to boost the power.
Liu Y & Kellis M. QtlWater: boosting molecular quantitative trait loci mapping power by incorporating recombination rate and chromatin conformation changes. In preparation.
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Install
git clone --recursive https://github.com/dnaase/QtlWater.git cd QtlWater mvn clean package -
Run the example test file
unzip test_data_zip.zip mv test_data_zip test_data perl QtlWater_pipeline.pl test configure.txtThis should produce the following files:
- cis-qtl.matrixEQtlAll.SampleSize-133.test.chr1.txt (MatrixEQTL result)
- cis-qtl.matrixEQtlAll.SampleSize-133.test.chr1.sig.sameChr.addCor.uniq.log10p_hic_recomb.afterQtlWater.fdr.txt (QtlWater FDR result)
- Java 7 (Oracle)
- R-3.0 or above (https://www.r-project.org/)
- Perl 5
- MatrixEQTL package in R (http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/runit.html or https://cran.r-project.org/web/packages/MatrixEQTL/index.html)
- bigWigAverageOverBed from UCSC utils (http://hgdownload.soe.ucsc.edu/admin/exe/)
Compilation requires mvn 3.0 or above
```
git clone --recursive https://github.com/dnaase/QtlWater.git
cd QtlWater
mvn clean package
```
- recombination rate big wig file, which could be download from 1000 Genome ftp fite
- Hi-C signal file, which could be download from (Rao et al. 2015 Cell)
perl QtlWater_pipeline.pl test configure.txt --mode 2 --ground_truth_data test_data/cis-qtl.matrixEQtlAll.SampleSize-133.test.chr1.txt --ground_truth_data_indexs 1 --ground_truth_data_indexs 2 --ground_truth_data_rawp 5 --ground_truth_data_fdr 6
perl QtlWater_pipeline.pl test configure.txt