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ma-compbio / GAGE-seq

Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq
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How do I separate K562 and GM12878 in KG-0210-PL1 scRNA-seq file #2

Open gmurtaza404 opened 5 months ago

gmurtaza404 commented 5 months ago

Hello, I am trying to reproduce some of the results from the paper. I am currently trying to separate all cell line datasets. I have been able to follow the instructions in the supplementary section to segregate K562-NIH3T3 mixture and process the MDS-L datasets. Currently I am unable to segregate GM12878 cells from the K562/GM12878 mixture. The details in the supplementary section suggests that they were segregated based on their "first round barcodes", how do I access these first round barcodes, and how do I get the mapping of these barcodes to cell lines?

Thanks!

yemingx commented 3 months ago

If you have the K562-NIH3T3 demultiplexed dataset, maybe you can align to the hg19/hg38 and mm10 combined genome and reproduce the Fig.1b of GAGE-seq. Then you can tell which cells are GM12878 cells.

yemingx commented 3 months ago

For K562/GM12878, you may have to run cell clustering, and get the pseudo bulk contact map for each cluster and compared with the GM12878 contact map. Then you can distinguish GM12878 from K562.