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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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Obtain bin by cell matrices from bulk WGS+ scDNAseq #11

Open kzb193 opened 7 months ago

kzb193 commented 7 months ago

Hello,

I have a 10x scDNAseq tumor data and a matched bulk WGS normal data. I would like to perform CNA analysis using Alleloscope. I am not sure on how to prepare the 'Bin by cell (sparse) matrices for tumor and normal samples' in step 4. Specifically,

1) are the bin-widths fixed e.g. "chr1-1-20000", or is there a way to construct the bins? 2) Given a set of bins, can you suggest a way to get the 'bin by 1' matrix from the bulk wgs bam file?

kzb193 commented 6 months ago

Hello, Can you please help me out on this issue?

Thanks.

seasoncloud commented 6 months ago

Hello!

Sorry for the late reply!! Please see the following answers--

  1. The bin-widths do not need to be fixed. The output from the 10x scDNA-seq preprocessing may already include a bin by cell matrix? You could check out this script for generating the bin coordiate file: https://github.com/seasoncloud/Basic_CNV_SNV/blob/main/scripts/Generate_bed.R and the chromosome size file here https://github.com/seasoncloud/Alleloscope/tree/main/data-raw

  2. Yes I used bedtools https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html# to get the bin by 1 matrix.

kzb193 commented 6 months ago

Thank you so much for your response, and the details. I will get back to you with further updates on this.

kzb193 commented 1 month ago

Thank you again for your help on this. It turned out that the normal WGS sample had some issues. So, I am focusing on using Alleloscope with the scWGS sample alone i.e., I do not have the normal sample. I think the tutorial of P5931 suits my case as it does not use "ref_counts". The tutorial has used each chromosome as a segment. Instead, is it possible to use the chromosome arms (1p,1q, etc.) as segments somehow?