Hi ! I did scRNAseq (10XChromium) of cancer cells and now I am looking for a simple way to split my FASTQ Files into celll specific FASTQ Files. Alternativley split my BAM File into cell specific BAM Files - because I need one FASTQ (BAM) File per cell in order to do perform variant calling on the single cell level. My goal is to obtain one single VCF file per cell.
Is there a build-in function in CellRanger for that? Are there any other tools to demultiplex my FASTQ/BAM Files using cell barcodes and split them into cell specific FASTQ/BAM Files?
Any help is highly appreciated! Thank you so much!