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SIG: Bioconductor Infrastructure for Base Modifications #35
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Updated description with
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@Shians I scheduled this for the Smillow Seminar Room 3:30 - 4:30 today |
I'm taking notes which I'll post here |
From the discussion it sounds like For a general description of modifications, if we want to look toward other projects for consistency, the NCBI C++ toolkit has an analogous
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For a dictionary of DNA or RNA nucleotide modifications have a look at the https://bioconductor.org/packages/release/bioc/html/Modstrings.html edit:
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Thanks, Felix! Your work on RNAmodR came up during discussions, but I forgot about ModStrings! |
Here's my notes from the day (copied below):
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RNAmodR is basically structured like this:
General ideas and experiences:
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@Shians fyi: It is probably quite easy to turn RNAmodR into a modR package and extend a separate RNAmodR and DNAmodR package. Let me know, if that might be of interest to you. |
Thanks Felix, I’m on vacation and will have a look at this next week to properly digest it. If memory may be a problem, I’ve been itching to learn some on-disk methods. |
@Shians Due to the recent changes in the At the same time I introduced the |
Introduction
I am a new PhD Student at the Walter and Eliza Hall institute in Melbourne, Australia. My project is based around methods and tools for the analysis of DNA methylation in long reads using Oxford Nanopore sequencers. My formal background is in statistics but I mainly work on developing software and have a keen interest in efficient and user-friendly computational methods and visualisation.
Expected attendees
Researchers who are interested in base modifications of all kinds, I am interested in DNA but the developed structure should equally support RNA modifications.
Should it be held during Developer Day
Probably
Description of the topic
(Will update this section after I do some more research and take suggestions)
I think there are things to keep in mind for this:
As far as I'm aware there's not a specialised widely supported Bioconductor structure for storing base modification information that also facilitates straightforward querying of common issues. The basics would be to ask for the methylation proportions in a specific region, there should be metadata within objects to separate groups for which this can be asked as well as reporting of coverage at the loci. Additionally it would be useful to query within-read methylation patterns, to inspect correlation between methylation sites within molecules. Compactness of representation is also going to be important, sparse or on-disk representations would be useful to consider, features and query performance probably take second place to storage size.
Desired outcome
I'd like to establish a set of queries of interest and a general abstract idea of what data structure(s) might be appropriate.
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