README.md

# Fiumara_BasePrimeEd2022_BARseq

Fiumara M, Ferrari F, Omer-Javed A, Beretta S et al.
**Genotoxic effects of base and prime editing in human hematopoietic stem cells.**
_Nature Biotechnology_ 2023.
- PMID: [37679541](https://www.ncbi.nlm.nih.gov/pubmed/37679541)
- DOI: [10.1038/s41587-023-01915-4](https://doi.org/10.1038/s41587-023-01915-4)
- Base Editors (HDR): [GSE220753](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE220753)

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### Analyses ###

Sequencing data were analyzed with the [_BAR-Seq2_](https://bitbucket.org/bereste/bar-seq2) pipeline, with the following parameters:
- `--trim-sequences --trim-opt '-m 50 -q 30'` to trim low-quality bases and keeping sequences having length >50bp;
- `--edit-distance 2`;
- `--min-count 2` to keep only barcodes having minimum count equal to 2.

The number of clones were calculated for each sample by normalizing the number of unique BARs by the sample VCN.</br>
SCID-repopulating cells (SRC) frequency (1 out of 'x') was calculated by dividing the HSPC t0 equivalent by the number of unique BARs retrieved in the long-term human graft in the BM.