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A tool to compute various coverage statistics given a .bed file (i.e. a CLIP or ChIP-Seq result) and a reference genome.
This project forked from alexamlie/bed_statistics
A tool to compute various coverage statistics given a .bed file (i.e. a CLIP or ChIP-Seq result) and a reference genome.
genewise_bed_coverage.py - compute coverage of a .bed file over all genes entrywise_bed_coverage.py - from the other direction, given a .bed file and 4 .bed files containing promoters, exons, introns, and repeat regions, calculate genomic partition of each entry in the .bed file (no UTRs) UPDATE THIS bed_gene_feature_coverage.py is the main script here. It is used to compute various coverage statistics given a .bed file and a reference genome, which can be in any format as long as you give a header file with the format for it. This can be generated by downloading a table from the UCSC genome browser and then putting the top line into the header file, like: head -n 1 ref_file.txt > ref_header.txt The script is run as follows: python bed_gene_feature_coverage.py reffile ref_format bedfile output log Where reffile and ref_format are the reference and header files described above, bedfile is the .bed file you want to compute statistics on, output is the path to the output file, and log is the path to a log file, which contains details of peak checking for debugging purposes.
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