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Published 20 hours ago • verified publisher icon seasoncloud

Obtain bin by cell matrices from bulk WGS+ scDNAseq

Open kzb193 opened this issue 10 months ago • 3 comments

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 avatar Apr 04 '24 14:04 kzb193

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

Thanks.

kzb193 avatar May 01 '24 13:05 kzb193

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.

seasoncloud avatar May 10 '24 04:05 seasoncloud

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

kzb193 avatar May 15 '24 02:05 kzb193