Matt Regner

Hi @wheaton5 I want to genotype scATAC-seq cells and specifically focus on non-coding genetic variants. Do you recommend performing freebayes variant calling restricted to non-coding regions first? Or would I...

Freebayes for non-diploid cancer cells

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Hi @wheaton5, If users are working with non-diploid cells, such as cancer cells that are aneuploidy (loss and gain), can users adjust the freebayes step as follows?: `freebayes -f ref.fa...

A super helpful tool for scRNA-seq analysis! Could SCCAF be used to solve the "cluster resolution problem" in scATAC-seq as well? Instead of genes, SCCAF could be used with variable...

How to assign optimal k value to a new variable?

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Hi @siyao-liu Can you suggest some commands to automatically return the optimal k value based on the convex hull without having to look at the diagnostic plot (i.e. for data...

scATAC-seq doublet detection

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Very useful and easy to use tool! I wanted to ask if DoubletDecon can be repurposed for scATAC-seq doublet detection. Theoretically, you could run DoubletDecon on the **gene activity matrix**...

Hi @jgranja24 @jeffmgranja I had a question regarding this sentence from the methods section: "Matching scATAC-seq-scRNA-seq pairs using Seurat’s canonical correlation analyses. To integrate our epigenetic and transcriptomic data we...