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 |