polya_liftover Version 1
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A Snakemake workflow for using PolyA_DB and UCSC Liftover with Cellranger.
Some genes are not accurately annotated in the reference genome. Here, we use information provide by the PolyA_DB v3.2 to update the coordinates, then the USCS Liftover tool to update to a more recent genome. Next, we use Cellranger to create the reference and count matrix. Finally, by taking advantage of the integrated Conda and Singularity support, we can run the whole thing in an isolated environment.
Please see our README for the full details!
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Version History
Version 1 (earliest) Created 17th Jan 2022 at 10:44 by Ryan Patterson-Cross
Associated with v2.0.1 of the GitHub repository. https://github.com/IMS-Bio2Core-Facility/polya_liftover/releases/tag/v2.0.1
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Views: 13642 Downloads: 532
Created: 17th Jan 2022 at 10:44
Last updated: 17th Jan 2022 at 14:21
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The Bio2 core is a scientifically complex facility that provides data analysis, scientific computing and data management support to a wide range of scientists within the Wellcome-MRC Institute of Metabolic Science (IMS) and across the wider scientific community in Cambridge.The remit of the core includes:Use, develop and maintain state of the art SOP and methods for the analysis (and visualisation) of scientific data.Provide assistance in biostatistics and experimental design.Mine and analyse the ...
Space: Independent Teams
Public web page: https://www.mrl.ims.cam.ac.uk/research/core-facilities/bio2-home/
