Skip to main content

Table 1 GOPHER parameters: The users may chose parameter settings that influence the design of probes and digests. In addition, approach-specific parameters can be chosen

From: GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution

Probe parameters  
Probe length Explanation: Length of probes.
  Default: 120 bp
Minimum GC content Explanation: The minimum proportion of G and C nucleotides.
  Default: 35%
Maximum GC content Explanation: The maximum proportion of G and C nucleotides.
  Default: 65%
Alignability Explanation: Maximum mean 50mer alignability.
  Default: 2
Digest parameters  
Margin size Explanation: Width of the outermost ends of digests that will be tiled with probes.
  Default: 250 bp
Minimum digest size Explanation: Smaller digests cannot be selected.
  Default: 120 bp
Minimum number of probes Explanation: At least this number of probes have to be placed in each margin of a balanced digest. The total number of probes in both margins of unbalanced digest must be at least twice this value.
  Default: 1
Allow unbalanced margins Explanation: Digest with unequal numbers of probes in each margin are selected during viewpoint creation.
  Default: False
Simple parameters  
Allow patching Explanation: Digests that are not well centered at the TSS will be patched during viewpoint creation.
  Default: False
Extended parameters  
Maximum distance upstream Explanation: Extension of the viewpoint in upstream direction
  Default: 5000 bp
Maximum distance downstream Explanation: Extension of the viewpoint in downstream direction.
  Default: 1500 bp