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Table 1 Summary of operations provided in pgltools

From: Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data

Method Description
intersect Find overlapping paired-genomic-loci from two PGL files
merge Merge nearby paired-genomic-loci within a single file and produce a column containing summary statistics requested through passed parameters (-c and -o)
subtract Find parts of paired-genomic-loci from a PGL file that do not overlap another PGL file
window Filter a PGL file to a particular genomic region
samTopgl Converts a sam file to a PGL file
coverage Find the coverage of a PGL file on another PGL file; usually used to find the coverage of reads from a PGL file derived from a sam file on a set of PGLs. The paired-genomic-loci from file 2 only need to overlap the paired-genomic-loci from file 1.
closest Find the closest paired-genomic-loci from a PGL file for each paired-genomic-loci in another PGL file
expand Expand both loci by a given size
intersect1D Find the paired-genomic-loci that overlap regions from a bed file
closest1D Find the closest paired-genomic-loci to a set of regions from a bed file
subtract1D Find the parts of paired-genomic-loci that do not overlap regions from a bed file
sort Sorts a PGL file for use with other PGLtools operations
formatbedpe Convert a bedpe-like file to a PGL file
formatTripSparse Convert a triplet sparse matrix file set to a PGL file
conveRt Formats the PGL file for use with the GenomicInteractions R package
browser Format a PGL file to be viewed in the UCSC Genome Browser
juicebox Format a PGL file to be viewed in juicebox
condense Convert a PGL file to a BED file with two entries for each PGL entry.
findLoops Convert a PGL file to a BED file with an entry containing the region from the start of anchor A to the stop of anchor B for intra-chromosomal PGLs, and an entry for each anchor for inter-chromosomal PGLs.