**Disrupting TIGIT by cytosine base editing enables effective and safe T-cell therapy for pancreatic cancer.**
2024.
- ENA [PRJEB79006]
---
### Analyses ###
Sequencing data were analyzed with [_CRISPResso2_](https://github.com/pinellolab/CRISPResso2).
- Pre-processing options: `–trim_sequences –trimmomatic_command trimmomatic –trimmomatic_options_string ’ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 MINLEN:100’` to get rid of low-quality positions (score < 30) and to remove Illumina adapters, keeping only trimmed sequences longer than 100bp
- Sequences were mapped to the input amplicon reference and the quantification window was set to 1bp around the cut site, as identified by providing the gRNA sequence. Computed alleles were quantified by measuring the number of reads and their relative abundance based on total read counts.
- Base editing options: `--base_editor_output --conversion_nuc_from <C/G> --conversion_nuc_to <T/A>` to measure the frequency of the expected nucleotide substitutions for the specific BE
CRISPResso2 output alleles were post-processed by correcting all the mismatch positions outside the quantification window and re-quantifying the total read counts and consequently the corresponding relative abundances.
Alleles showing a relative abundance lower than the false positive threshold (set at 0.2% based on untreated samples) were filtered out.
