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rargelaguet / scnmt_gastrulation

scNMT-seq gastrulation
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Question: Annotation Info #1

Closed LiNk-NY closed 3 years ago

LiNk-NY commented 4 years ago

Hi Ricard, @rargelaguet CC: Al @ajabadi Thank you for making this data available to the SC research community. This is a great resource for advancing the multi-modal analysis of single cell data.

I would like to be able to reproduce the summarization of methylated regions. I see the code for doing so under load_data.R and load_annotations.R but I am not sure where the annotation datasets are coming from. They look like these below. Are these publicly available somewhere? 

# IMPORTANT: For every CpG/GpC site, the the rate must be 0 or 1

# (2) genomic feature annotation files in BED6 format
#   chr start end strand id anno
#   1   3531624 3531843 *   CGI_1   CGI
#   1   3670619 3671074 *   CGI_2   CGI
#   1   3671654 3672156 *   CGI_3   CGI

Thank you for your help. With your permission (and attribution of course), we would like to distribute the data as an ExperimentHub package in Bioconductor.

Best regards, Marcel

rargelaguet commented 4 years ago

Hi Marcel, I am sorry for the slow reply. The genomic context annotations can be downloaded with the parsed data set. They are in .../features/genomic_contexts. In that folder there is also a README file which explains where do the annotations come from.

Happy for this to be distributed as an ExpertimentHub, thanks!

jonathangriffiths commented 4 years ago

Hi @LiNk-NY

Sorry to jump in here, but do you know how this is going? I was thinking about incorporating this dataset into our existing MouseGastrulationData package (https://bioconductor.org/packages/release/data/experiment/html/MouseGastrulationData.html) alongside another ATAC-seq dataset that was recently released. However, we shouldn't be duplicating data on ExperimentHub - so if you're nearly there, then I can leave it to you. Alternatively, we might be able to merge your work into MGD via pull request, if you are interested.

Thanks, Jonny

LiNk-NY commented 4 years ago

Hi Jonny, @jonathangriffiths We already have the package submitted to Bioconductor. See: https://github.com/Bioconductor/Contributions/issues/1470

LiNk-NY commented 4 years ago

Hi Ricard, @rargelaguet

I was able to post the MultiAssayExperiment object on ExperimentHub see the issue posted above to follow progress, if interested.

OTOH, when trying to reproduce the summaries, the link you provided does not work for me. I don't see ../features/genomic_contexts at that link or in the tarballs. Perhaps there is an admin layer that doesn't allow access? Thank you for your help.

jonathangriffiths commented 4 years ago

Super, I'll make sure to point people towards your package

Jonny

aljabadi commented 4 years ago

Hi @LiNk-NY,

Here is the link to my copy of the .bed files in gastrulation/features/filt.

https://cloudstor.aarnet.edu.au/plus/s/B2fZNpBErhepXOz

Hope it helps

Al

LiNk-NY commented 4 years ago

Thanks Al! @ajabadi