Maps loop loci from ChIA-pet/Hi-C/etc. experiments across samples, which may be different species and/or cell types. Uses the bnMapper algorithm for cross-species mappings.
License: MIT License
Python 87.14%C 0.41%Shell 0.80%Cython 11.65%
maplooploci's Introduction
mapLoopLoci
Apply conservation class labels to loop loci mapped across species and/or cell types.
Map loop loci, in bedpe format, across cells and/or species. Input loops are
labelled according to whether they are conserved (i.e., left and right anchors
in the query both map to left and right anchors in the same target loop,
allowing for possible inversions), partially conserved (one anchor is used in
both species/cells), or species/cell-specific (neither anchor is used in the
other species). Cross-species mappings are performed using the bnMapper
algorithm, to map features from the target species to the query species of a
chain alignment file.
Ignore elements with an insertion/deletion of this or bigger size. (default: -1 -- accept all gapped alignments)
-v
--verbose
{info,debug,silent}
Verbosity level (default: info)
-k
--drop_split
If elements span multiple chains, silently drop instead of reporting the segment with the longest overlap. (This is the default behavior for bnMapper.) (default: False)
-m
--min_overlap
INT
Minimum amount of overlap to consider a pair of query/target anchors as shared. (default: 1)
-w
--slop
INT
Number of bases added up/downstream of query and target regions to enable flexible mapping. (default: 0)
Output
Column(s)
Description
1-9
Input BEDPE fields
10-13
Orthologous coordinates of the LEFT anchor in the target genome. (chrom, start, end, strand)
14-17
Orthologous coordinates of the RIGHT anchor in the target genome. (chrom, start, end, strand)
18-22
Target loop anchor overlapping LEFT anchor of query loop. (name, anchor_in_target ("l"eft/"r"ight), chrom, start, end)
23-27
Target loop anchor overlapping RIGHT anchor of query loop. (name, anchor_in_target ("l"eft/"r"ight), chrom, start, end)
28
Conservation class assignment.
Conservation classes
Class
Description
C
Conserved. Both anchors map and are assigned to the same target loop.
B2
Both anchors map, but are assigned to different target loops.
B1
Both anchors map, but only one is assigned to a target loop.
B0
Both anchors map, but neither is assigned to a target loop.
N1A
Semi-species-specific. Only one anchor maps to the target genome and the mapped anchor is used in target as a loop anchor.
N1B
Species-specific, semi-mapping. Only one anchor maps to the target genome and the mapped anchor is not used in target as a loop anchor.
N0
Species-specific, non-mapping. Neither anchor maps to the target genome.
The first six columns represent the genomic positions, the eighth column should be the interaction counts, and the ninth column represents the p-values。
I don't quite understand the meaning of the seventh column.
what does 99179/ 99186/ 99175 mean
chr22 18312801 18313021 chr22 18558869 18559119 99179 105 0.000000
chr22 18941930 18942280 chr22 19132279 19132487 99186 8 0.032835