scTE: error: argument -CB: invalid choice: 'CB:Z' (choose from CR, CB, False)

[katsikora]

Dear Authors,

thank you for providing scTE.

I am running scTE on a bam file output by cellranger 8.0.1. The bam file head looks like this:

A00931:878:HCWJ7DRX7:1:2144:18078:23970	16	chr1	3000332	255	101M	*	0	0	TCCTTTTTCATTTCTGATTTTGTTAATTATAGTACAGTCCCTATGCCCTCTAGTTAGTCTGGCTAAGGGTTTATCTATCTTGTTGACTTTCTCAAAGAACC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	NH:i:1	HI:i:1	AS:i:99	nM:i:0	RG:Z:E125mCon:0:1:HCWJ7DRX7:1	RE:A:I	xf:i:0	CR:Z:AAGTACGGTGACTCTG	CY:Z:FFFFFFFFFFFFFF:F	CB:Z:AAGTACGGTGACTCTG-1	UR:Z:CTCCGGTAACAA	UY:Z:FFFFFFFFFFFF	UB:Z:CTCCGGTAACAA

i.e. the cell barcode is stored in the CB:Z tag and the UMI in the UB:Z tag.

Running scTE with default settings raises the error:

The input file possorted_genome_bam.bam has no cell barcodes information, plese make sure the aligner have add the cell barcode key, or set CB to False

While running scTE with -CB CB:Z -UMI UB:Z gives:

scTE: error: argument -CB: invalid choice: 'CB:Z' (choose from CR, CB, False)

Could you kindly assist me with this issue?

Best wishes,
Katarzyna