New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

How to include the lane index in STARsolo count matrix barcodes.tsv? #2243

Open

mkarikom opened this issue Nov 19, 2024 · 0 comments

mkarikom commented Nov 19, 2024

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

The text was updated successfully, but these errors were encountered:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment