Fiumara M, Ferrari F, Omer-Javed A, Beretta S et al.
**Discovery and mitigation of genotoxic effects of base and prime editing in human hematopoietic stem cells.**
_Nature Biotechnology_ 2023.
- 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.
