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seasoncloud / Alleloscope

Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On scATAC-seq data, Alleloscope allows integrative multi-omic analysis of allele-specific copy number and chromatin accessibility for the same cell.
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3. scATAC-seq #5

Open FanBioinformatics opened 2 years ago

FanBioinformatics commented 2 years ago

Hi there,

Thanks for providing such an interesting tool for the research community. I am testing the pipeline on scATAC-seq tumor samples only. How to work around "Step2. Unbiased segmentation based on matched WES/WGS data" in the tutorial? Simply skip it?

Best, Huihui

seasoncloud commented 2 years ago

Hello, sorry for the later response and thanks for your interest in Alleloscope! Currently, we only tested Alleloscope's performance using an unbiased segmentation from either matched WGS/WES data or any segments you think there is a CNA. If you don't have any segments, the tool will use each chromosome as the segments by default. However, the performance of estimation on each chromosome might not be very ideal and has not been thoroughly tested yet. We are also trying to perform segmentation on scATAC-seq itself for the later version. We will update the tool once it is ready!