PrimerS-JuJu

Tools to assist with designing multiple RT-PCR primers for full-length isoform amplification.

Package is currently alpha-quality and requires a bit manual setup to run.

This package builds on primer3 and Primer3-py.

Untergasser, Andreas, et al. "Primer3—new capabilities and interfaces." Nucleic acids research 40.15 (2012): e115-e115. doi: 10.1093/nar/gks596

Licensed under GPL v2 to comply with the primer3 license.

Install in a python virtualenv

CFLAGS=-std=c99 pip install git+https://github.com/diekhans/PrimerS-JuJu.git

primer3-py needs -std=c99, at least on some systems.

Addition requirements

• available from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

  • bigBedNamedItems
  • bigBedToBed

• available from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/

  • gfPcr
  • gfServer (if not using an assembly in the UCSC browser)