Table 1 Summary of operations provided in pgltools
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. |