Kaitlyn’s notebook: Geoduck reproductive development primer design

After testing the previous primers, it was decided that the primers were not specific enough for successful sex or reproductive stage identification. I am going to design new primers with the most recent geoduck genome version of all proteins listed in Fig. 6.

I am following Sam’s Jupyter post  (downloadable here) and Github post. I am focusing on primer design and primer specificity, as the fasta file containing the 8 proteins in Fig 6. has been created.

I used jupyter notebook to annotate code and explain shell to understand new commands.

        1. Download
          • pyfaidx – splits multi-FastA into individual FastA files
          • Primer3 – performs primer design
          • EMBOSS(installation issue linked) – checks primer specificity against entire transcriptome
            • installed without X11 support (problem with X11 headers)
        2. Split FastA into multiple FastAs using pyfaidx
        3. Design primers with Primer3 (issue with code)
        4. Check specificity using EMBOSS
          • Problem with primersearch function