Understanding the barcodes command

[Thapeachydude]

Hi,

I'm trying to demultiplex a series of pools (9-11 donors) with known genotypes based on WES and WGS data. Some of the pools work really well, while others struggle a bit. An issue that I see, the doublet rate in some of the pools is relatively high (quite obvious cell blobs in the middle of a UMAP), this seems to "confuse" souporcell during the clustering, as some SNP clusters are only assigned to these blobs.

Since these are quite obvious doublets, I would try and remove them before running souporcell.
Hence, is there a way to "subset" the number of barcodes souporcell runs on? As, does the barcodes.tsv file provided already subset the number of barcodes processed or would I have to manually subset the bam file before providing it to souporcell.

Cheers and many thanks,
M

[wheaton5]

Yeah, just make a new barcodes.tsv and it will only run on those.