GeFF

Genomic Feature Finder

how to use: mkdir build cd build cmake .. make

copy bigWigInfo to resource/bin copy bedGraphToBigWig to resource/bin copy bigWigToBedGraph to resource/bin

Plan

user input: input_list chrom_sizes = cannonique - chrY bin = 10000 include = all exclude = none

to_hdf5 {input_list.txt} " "{chrom_sizes} " "{output.hdf5} " "{bin_size}\n");

to_zscore {input_list.txt} " "{chrom_sizes} " "{input.hdf5} " "{output.hdf5} " "{bin_size} " "{include.bed} " "{exclude.bed}\n");

corr {input_list} " "{chrom_sizes} " "{input.hdf5} " "{output.results} " "{bin_size}\n");

make_matrix.py {list_path} {chrom_size} {corr_path} {output_path}"