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Pick primers without 'CG' in them #18

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haseebz opened this issue Aug 6, 2021 · 2 comments
Open

Pick primers without 'CG' in them #18

haseebz opened this issue Aug 6, 2021 · 2 comments

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@haseebz
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haseebz commented Aug 6, 2021

I am using Primer_TK to design primers that can be used for methylation detection. To achieve this I would like primers that do not have consecutive 'CG' nucleotides in them. Is there a way to do this?

@haseebz
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haseebz commented Aug 10, 2021

Adding a suggestion on this.
Since primer_tk uses primer3 parameters to pick primers, is it possible to use EXCLUDED_REGIONS from the primer3 options to exclude CGs from primer design?

@haseebz
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haseebz commented Aug 12, 2021

I have figured out one way we can do this. We can use SEQUENCE_EXCLUDED_REGION= in the primer3_input file. But doing this manually for a few sequences is easy. How can we do this for a larger input file?

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