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jdhotopp / tp.py-Direct-RNA-Sequencing-Manuscript-

Repository for the manuscript describing tp.py and direct RNA sequencing
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Provide actual Python Code of the algorithm #1

Open mwittchen opened 3 days ago

mwittchen commented 3 days ago

Hello,

this repository belongs to the publication "Deciphering transcript architectural complexity in bacteria and archaea" (https://doi.org/10.1128/mbio.02359-24) . You mention in the publication's abstract that you "[...] developed an algorithm for transcript prediction called tp.py using it to predict transcripts [...]". Nevertheless the algorithm is not published, there are no URL or other hints where to find the actual python algorithm. This repository only contains the R and Perl code for creating the diagrams of the publication.

So please publish the python algorithm for transcript prediction as this algorithm is the center piece of your publication!

All the best!

adkinsrs commented 3 days ago

Hi @mwittchen,

The algorithm can be found at https://github.com/Dunning-Hotopp-Lab/Direct_RNA_Sequencing and I have informed the maintainer of this repository to add the link in the README file.

jdhotopp commented 3 days ago

Thanks Shaun!

From: Shaun Adkins @.> Sent: Thursday, September 26, 2024 9:56:55 AM To: jdhotopp/tp.py-Direct-RNA-Sequencing-Manuscript- @.> Cc: Subscribed @.***> Subject: Re: [jdhotopp/tp.py-Direct-RNA-Sequencing-Manuscript-] Provide actual Python Code of the algorithm (Issue #1)

Hi @mwittchenhttps://github.com/mwittchen,

The algorithm can be found at https://github.com/Dunning-Hotopp-Lab/Direct_RNA_Sequencing and I have informed the maintainer of this repository to add the link in the README file.

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mwittchen commented 3 days ago

Hi @adkinsrs ,

thank you for the link to the algorithm. I didn't find it in the publication. Did I miss it?

adkinsrs commented 3 days ago

No, this was on us. I don't think any of us had noticed the "manuscript" repository (this one) was missing the algorithm link.

@jdhotopp can you add the algorithm link to the README for this repo to avoid future similar questions? I do not have permissions to make edits to this repo (unless I fork and pull request).