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I have been using seqfold to design oligo constructs, but have run into issues when I use degenerate bases (like in unique molecular identifiers, UMIs). Would there be a straightforward way to allow f…
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The basic idea:
I think it might be useful to allow users to upload a spreadsheet with oligos they have already designed. Cloning strategies can have multiple steps, with many oligos being used, and …
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Hello,
I have encountered an issue while trying to design oligos for my experiment. The script threw an IndexError, as shown in the output below.
The fasta file is the same I used for aligning, t…
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POST `/primer_design/whatever?options` -> submit sequences
TODO:
* [x] Add tests
* [x] Add Gibson functionality:
* [ ] This should allow for the user to specify which fragments you want to amp…
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Dear,
I completed the test running without probe successfully. Now, I am running the test to obtain primers and probes with the option: internal_oligo: --make-oligo 1 --int-opt-size 20 --int-opt-tm…
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Dear developers:
openDBA has many applications, which are very interesting. Nanopore provides a kmer model for generating standard nanopore signals. By providing a sequence based on this kmer model, …
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Hi, Akihiro
I met some problems when I try to use DAJIN in a benchmark between different nanopore genotyping methods.
1) I run your method on the server and I don't have the sudo permission so I can…
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@tnrich, I created this ticket to support its sister ticket in HDE: https://github.com/TeselaGen/hde/issues/954
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**Visualizing functional vs. physical elements**
Functional elements (shown wi…
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There's some really nice plotting functions in the new AgamPrimer package by @sanjaynagi for investigating whether there is any variation within a specific genome region that might affect primer bindi…
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We should provide the user with a complete list of oligo to order and primers