e-manduchi

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Follow up #8260 - reclustering using SCT - v5

Hello, I too am interested in following-up on this question as I am in a similar situation. I want to draw DimPlots with umap reduction for different subsets of an...

Follow up #8260 - reclustering using SCT - v5

Hello, I proceeded as I've outlined above.

Clarification on 'Warning: To many values of z. Using 2D polygons'

Thank you for your response. I had checked previously on this and the z values in my file are discrete, precisely they are all integers from 0 to 8.

Clarification on 'Warning: To many values of z. Using 2D polygons'

Thank you!

clarification on apparent discrepancy between snp.vcf and bedmethyl outputs

Thank you for your response. Indeed I was expecting an N_diff of at least 10 in the bedmethyl file. Here is the IGV screenshot for the region containing the C...

clarification on apparent discrepancy between snp.vcf and bedmethyl outputs

In the above screenshot, reads are arranged by alignment quality. How would you like me to share the bam file with you @ArtRand?

clarification on apparent discrepancy between snp.vcf and bedmethyl outputs

I've emailed you the bam, I appreciate your help!

clarification on apparent discrepancy between snp.vcf and bedmethyl outputs

P.S. This issue was also posted on https://github.com/epi2me-labs/wf-human-variation/issues/283.