3. scATAC-seq

[FanBioinformatics]

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]

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!