Adapting to Split-seq (Parse Biosciences)

ucagenomix / sicelore-2.1

MIT License

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Adapting to Split-seq (Parse Biosciences) #14

Open kwglam opened 9 months ago

kwglam commented 9 months ago

I am trying to adapt sicelore-2.1 to assign barcodes and umis on single-cell nanopore long-reads barcoded using Parse Biosciences. However, the read structure of Parse (polyA-BC-UMI-adapter) is different from that of 10x 3' (polyA-UMI-BC-adapter). Do you have any recommendations that I can change in the java scripts? Thanks!

RainerWaldmann commented 9 months ago

Parse uses multiple barcodes separated. by a spacer. While this is feasible, it would require major changes to the barcode assignment strategy.

kwglam commented 9 months ago

Does it work if I feed a list of barcode+spacer (63nt) for barcode assignment? I am curious what I can change to look for UMIs (searching regions downstream of BC instead of upstream?).