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NinaGXie / SADDLE

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fromGCAT issue #1

Open dsimps1993 opened 2 years ago

dsimps1993 commented 2 years ago

Hi,

I'm an absolute novice when it comes to Matlab. I tried running the Dimer Identify script with a list of primers I've already developed. However, the PrimeNumberHash function fails as it can't run the rep = fromGCAT(text) line. Is fromGCAT a function that has to be defined somewhere? I can't find it anywhere else in your scripts and nothing comes up on Google when I search for it.

On another note unrelated to this particular issue, as to why I'm using your package. Essentially I already generated 102 primer pairs separately with PrimerSuite as I needed primers for bisulphite converted DNA. Of course, however, running all 102 primers together in a PCR leads to primer dimers. I was wondering if it's possible to use your package in part to work out if I can split the primers into say, 3 or 4 configurations, so that I can run 3 or 4 multiplexed reactions per sample instead.

Let me know if you have any insight on this, and thank you in advance for your help!

Daniel Simpson

NinaGXie commented 2 years ago

Hi Daniel,

Thank you for the comments. And apologize for the late reply. We've added fromGCAT function to the folder.

Our data analysis code can't be used for generating primers, instead, it's used for analyzing NGS data to see if there are any dimers/non-specific amplicons in the NGS library.

Best, Nina

yizhenlinqq commented 2 years ago

Dear Nina,

i am studying in "Designing Highly Multiplex PCR Primer Sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE) these days," and i really interstered in algorithm of reducing the primer dimer, I would like to ask if there are open source for generating primers to refer to?

Please Let me know if have any insight on this, and thank you in advance for your help!

Best regards, Yizhen

Research Associate / Advanced Research Department
Credo Diagnostics Biomedical Pte. Ltd. Taiwan Branch

NinaGXie commented 2 years ago

Dear Yizhen,

Thanks for reaching out. For algorithm source code, please reach out to the corresponding author for further information. As mentioned in our paper, we provide code to the academic institution under NDA.

Best, Nina

On Thu, Apr 21, 2022 at 10:27 PM yizhenlinqq @.***> wrote:

Dear Nina,

i am studying in "Designing Highly Multiplex PCR Primer Sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE) these days," and i really interstered in algorithm of reducing the primer dimer, I would like to ask if there are open source for generating primers to refer to?

Please Let me know if have any insight on this, and thank you in advance for your help!

Best regards, Yizhen

Research Associate / Advanced Research Department Credo Diagnostics Biomedical Pte. Ltd. Taiwan Branch

— Reply to this email directly, view it on GitHub https://github.com/NinaGXie/SADDLE/issues/1#issuecomment-1106024912, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQDCXOBSQRLELZRBA5Q4TITVGI2FXANCNFSM5OYWOZZA . You are receiving this because you commented.Message ID: @.***>

yizhenlinqq commented 2 years ago

Dear Nina,

Thanks for your reply. I will connect corresponding author later.

Best regards, Yizhen