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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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about cell counts in somatic SNV output(chr*.putativeSNVs.csv) #35

Open hanjun98 opened 10 months ago

hanjun98 commented 10 months ago

Hi, first, thank you for interesting tool to use in single cell

I have a question about SNV output(chr*.putativeSNVs.csv).

When I put input bam file, bam file have 8923 unique cell barcodes, but When I got a chr*.putativeSNVs.csv, they just have 5704 unique cell barcodes

So I'm curiouts about how to call up cells in chr.putativeSNVs.csv? Is it have just cells with at least one variant, so 3219(8923- 5704) cells are not in the output file(chr.putativeSNVs.csv) because the variant is not called? or bugs, or problem of my technique?

All output file(chr.putativeSNVs.csv) have 5704 unique cell barcodes

I'll be waiting for your answer🥺 Thank you for reading!

jinzhuangdou commented 10 months ago

Monopogen indeed only extracts cells specified with option -l CB_7K.maester_scRNA.csv. Could you check how many cells in the file feed to the option -l? In addition, Monopogen has an option '-k' (with 0.8 as default value). If you want to use all cells you need to set '-k 1'.

parser_somatic.add_argument('-k', '--keep', required= False, default=0.8, help="The proportion of reads kept for somatic calling. The cell will be sorted based on reads detected and cells with fewer reads will be removed.")

jinzhuangdou commented 8 months ago

Could you try the new version which can improve the cell count detection using all cells?