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.
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pyfaidx
– splits multi-FastA into individual FastA filesPrimer3
– performs primer designEMBOSS
(installation issue linked) – checks primer specificity against entire transcriptome- installed without X11 support (problem with X11 headers)
- Split FastA into multiple FastAs using
pyfaidx
- Design primers with
Primer3
(issue with code) Check specificity using EMBOSS- Problem with
primersearch
function
- Problem with
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