This is some scripts for indel calling of SpCas9 for SURRO-seq.
- extract_reads_from_BAM.py Filter the reads that match the reference sequence from the aligned BAM file.
- remove_synthesis_error.jl According to WT, remove the synthesis error.
- get_indel_profile.jl Print indel profile for each trap oligos.
- remove_sequencing_error.jl Remove sequencing errors according to indel profile.
These scripts were developed by Pan xiaoguang and Luo yonglun for Massively Targeted Evaluation of Therapeutic CRISPR Off-Targets in Cells at the Qingdao-Europe advanced institue of life science