atlasxomics / clean_latch

Latch.bio workflow for remediating lane artifacts in spatial ATAC-seq experiments
MIT License
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Add imputation MVP #10

Closed jpmcga closed 8 months ago

jpmcga commented 1 year ago

Runs:

jpmcga commented 1 year ago

We tested 'average of neighbors' algorithm with D01355, D01270; resulted in the imputed tixels clustering out with neighbors for tixels in heterogenous regions (cluster 1, below). Tixels in homogenous regions looked ok. Let's try two different approaches to resolve artifact clusters,

  1. Remove diagonal neighbors from averaging so only direct neighbors used in imputations,
  2. New algorithm: copy exactly the direct neighbor (no diagonal) with the higher fragment count.

@JoshuaBAtlas

image
jpmcga commented 8 months ago

Completed for single lane in https://github.com/atlasxomics/ATX_impute/tree/main