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jon-xu / scSplit

Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
MIT License
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compare mixed samples together #28

Open laurajaras opened 3 months ago

laurajaras commented 3 months ago

Hi, I performed the workflow on multiple mixed samples, retrieving correctly the different genotypes, per sample. I was wondering what you can suggest to compare the different mixed samples, that should contain the same genotypes.

Genotype A in sample 1 Genotype A & B in sample 2 Genotype A & C in sample 3 etc.

Does the only way would be to merge the raw bam files? Or is there a way starting from the vcf or the scSplit_P_s_c.csv (from run function) or scSplit.vcf (from genotype function)

Thanks in advance for your reply, anf thanks for your tools which is exactly what I was looking for !

jon-xu commented 3 months ago

Hi, thanks for your interest in our tool! I am not very sure whether I understand your need clearly. Did you mean you want to demultiplex sample 1, 2, 3 which themselves are mixed samples with different genotypes? If genotype A is appearing in all three samples, maybe you want to give input to the script with -c parameter if you have a list of SNVs which is not representative for genotype A? Would that help?