How to include the lane index in STARsolo count matrix barcodes.tsv?

Question

[mk]

How can I make sure that the lane index is included in the STARsolo count matrix barcodes list?

If I run CellRanger and STARsolo on the same set of FASTQs I get full barcodes in CellRanger output:

(base) [mkarikom@gl1515 mkarikom]$ zcat 2024-05-14_rxn1_S1_Cellranger/outs/raw_feature_bc_matrix/barcodes.tsv.gz|head
AAACCAAAGAAACCAA-1
AAACCAAAGAAACCCC-1
AAACCAAAGAAACGGT-1
AAACCAAAGAAAGGTC-1
AAACCAAAGAAAGTCA-1
AAACCAAAGAAATCAG-1
AAACCAAAGAAATGGC-1
AAACCAAAGAAATTGG-1
AAACCAAAGAACAGAC-1
AAACCAAAGAACAGGT-1

But STARsolo is only reporting the nucleotide sequence without the lane index:

(base) [mkarikom@gl1515 mkarikom]$ head 2024-05-14_rxn1_S1_Solo.out/Gene/raw/barcodes.tsv
AAACCAAAGAGTACGG
AAACCAAAGATTCAGT
AAACCAGCAAGCTGGG
AAACCAGCACCGTTAG
AAACCATTCAATGCGC
AAACCCATCAATATTG
AAACCCATCCACTACT
AAACCCATCCCTGATT
AAACCCATCCGACTAA
AAACCCATCGGCTCTC

[swbarnes2]

Why do you want to do this? Does Illumina even make instruments anymore where you can have one sample in one lane, and a different sample in a separate lane of the same run?

Answer 1

[swbarnes2]

If you combine two samples together, the -1 and -2 at the end of cell barcodes will matter, so you know what cells came from what samples, especially because there is a non-zero chance that two different samples will have a few cells that happen to share the same cell barcode.

Answer 2

[jared.andrews07]

Where are you getting the info that the -1 corresponds to the lane? Because it doesn't.

From the 10X site:

The cell barcode CB tag includes a suffix with a dash separator followed by a number: AAACCCAAGGAGAGTA-1 This number denotes the GEM well, and is used to virtualize barcodes in order to achieve a higher effective barcode diversity when combining samples generated from separate GEM well channel runs. Normally, this number will be "1" across all barcodes when analyzing a sample generated from a single GEM well channel. It can either be left in place and treated as part of a unique barcode identifier, or explicitly parsed out to leave only the barcode sequence itself.

So more than likely, that suffix (or lack thereof) isn't providing you any additional info.

[mk]

thanks, so how do i make starsolo report the NNNNNNNN-i index of the gem well for barcode NNNNNNNN?