starSolo with UMIs only?

[David DeTomaso]

Is it possible to run starSolo with UMIs only?  We're using an RNA-seq protocol with UMIs but they aren't single-cell.  I'd like to use STAR for alignment and to collapse the UMIs for the count matrix, but I'm unsure the best way to configure without cell barcodes.  Is running with a 0-length cell barcode (as specified with soloCBlen) supported?

- David

[Alexander Dobin]

Hi David,

0-length barcode will not work. You can hack it by adding a constant base (say "A") at the end of your barcode read, and specifying it with --soloCBstart and --soloCBlen 1.

However, if you have a large number of reads, the 1 mismatch UMI deduplication may become inefficient - it scales quadratically with the number of UMIs.

Cheers

Alex