Version 1

Workflow Type: Snakemake

polya_liftover - sc/snRNAseq Snakemake Workflow

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!

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: 3191   Downloads: 18

Created: 17th Jan 2022 at 10:44

Last updated: 17th Jan 2022 at 14:21

Last used: 28th Nov 2022 at 05:46

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