Capture Oligo Design
The design.py module consists of three classes for Capture-C oligo design.
- Capture: designs oligos for a standard Capture-C experiment. The user supplies a list of viewpoint coordinates, and oligos are generated adjacent to the flanking recognition sequence of a specified restriction enzyme.
- Tiled: designs oligos for multiple adjacent restriction fragments across a specified region of a chromosome, or for the entire chromosome. If Tiled is run in contiguous mode, oligos are generated independent of restriction fragments and are instead generated for a user-specified step size, in an adjacent manner.
- OffTarget: designs oligos to capture DNA surrounding potential CRISPR off-target cut sites to allow for efficient sequencing to determine off-target activity.
These three classes all generate oligo sequences, based on different underlying behaviours. When run from the command line, design.py uses methods from the Tools class in the tools.py module, in a pipeline that checks the off-target binding and repeat content of the oligos. This information is output in a file called oligo_info.txt; oligo sequences are written to a FASTA file called oligo_seqs.fa
Installation:
To start using oligo, either clone the GitHub repository or download the latest release.
Requires:
For full documentation, see http://oligo.readthedocs.io
