Primer-based barcode retrieval and counting from barcoded samples
Tools used:
- bbduk
- NextFlow
- R
- singularity
This pipeline was used for retrieving barcodes from mouse blood cells. Stem cells were barcoded and then implanted into mice with flushed blood cells. Barcodes allowed for analysis of patterns in stem cell specialisation across blood cell types.
It can be used for any experiment where barcodes of known length are preceeded with a known primer.