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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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Tutorials for UXM fragment-level deconvolution #6

Closed willtc10 closed 1 year ago

willtc10 commented 2 years ago

Hi, Thank you for all the codes and tutorials.

I would like to ask if you have any plan updating tutorials about UXM fragment-level deconvolution?

Is the atlas in the unpublished supplementary? Can I use the deconvolution algorithm in Moss et al. (2018) to deconvolve after having the reference atlas from wgbs tools?

nloyfer commented 2 years ago

Absolutely! I will publish the UXM fragment-level deconvolution repository - code and tutorial - as soon as the paper gets accepted for publication. Hopefully soon.

Regarding the atlas - Processed files for the 207 samples were deposited to GEO and are available at GSE186458. Accessing the raw data (fastq files) will be possible once the paper is published.

julienlag commented 1 year ago

Hello! Meanwhile, could you please recommend a similar WGBS-based tissue deconvolution software, if it exists?

nloyfer commented 1 year ago

Hi, Our paper finally got accepted.

raw data

The fastq files are now being deposited to EGA. The accession will be published with the paper, any day now.

pat files

I uploaded all the pat files to GSE186458.

Deconvolution

The UXM deconvolution repository is now available here: https://github.com/nloyfer/UXM_deconv It includes a reference atlas and the code. Should be pretty straightforward to download and run it on your own data.

Other fragment-level deconvolution methods

I don't know any other published methods (at the moment), other than Celfie. I haven't tried it yet, but based on their previous work I bet it's good.