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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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Question of prepare input files #2

Open Ping-lin14 opened 3 years ago

Ping-lin14 commented 3 years ago

Hi, My scDNA data comes from the Mission bio platform, and "barcodes.tsv" or any file in the same format will not be output in Tapestri Pipeline. Is there any way to help me generate "barcodes.tsv"?

seasoncloud commented 3 years ago

Hello,

I checked the mission bio website and saw this page: https://support.missionbio.com/hc/en-us/articles/360045939853-Pipeline-output-files-overview Not sure if you got output files the same as those listed here. There is a file "barcode.cell.coverage.tsv". It seems to include cell barcodes of each cell based on the description. If this is the case, you could generate a tsv/ txt file with one column, each line indicating different cell barcodes.