Questions about single-cell barcoded BAM, PREFIX and the "CB:Z:" tag

raphael-group / chisel

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links

BSD 3-Clause "New" or "Revised" License

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Questions about single-cell barcoded BAM, PREFIX and the "CB:Z:" tag #29

Closed zhaoxiaofei closed 8 months ago

zhaoxiaofei commented 1 year ago

Hi chisel-devs,

I have a question about the single-cell barcoded BAM file which is the main input to chisel: what if the raw data do not contain any barcode information? For examples, in the sequencing data with accession SRA018951.105, different cells simply have different FASTQ filenames. In this case, can I just fill in dummy barcode into the FASTQ or BAM files?

Best, Xiaofei

simozacca commented 8 months ago

Yes, dummy barcodes can be used (they just need to be unique identifiers for each cell), and we reccomend the use of chisel-prep command that does this processing automatically for you.