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Question Regarding Cell-level Information of 10x data #14

Open jiazhen-rong opened 4 months ago

jiazhen-rong commented 4 months ago

Thanks for creating the tool! I was trying scAllele on public 10x scRNA data and was able to get the output files (intronic_parts.bed, mi_summary.tab, read_cluster_info.tab and vcf). However, the vcf file seem to be for bulk-level. If I want to see SNPs + indels at cell level, shall I split the bam file into individual cells? Or maybe the cell level info is already stored in the output files?

ManuelMoradiellos commented 2 months ago

I was wondering exactly the same thing!

I'm my case I'm working with public smart-seq2 data, but I'm trying to split the BAM into individuals ones although by the way that scAllele works I think it might not return many results due to the diminished number of reads per allele/region.

Another idea that I have is trying to parse the sequenced reads so I can obtain chr coordinates to each read and then assign the variants to those cells that have the alternative alleles. But I'm not sure if I'll be able to manage to do so...