Insertion site profiling analysis method for three active R2 retrotransposons in human cells

Bash pipeline for R2 NGS insertion-specificity analysis: merges two biological replicates per R2 retrotransposons (R2-1_TG, R2-1_TSP, R2-1_TUr), then runs adapter trimming, plasmid alignment (BWA-SW), chimeric filtering, 28S rDNA alignment (BWA-MEM), UMI counting, and human genome (hg38) alignment with fragment deduplication and UMI counting. Outputs one directory per R2. Requires: cutadapt, BWA, samtools, seqkit, cdbfasta/cdbyank, Perl, and five Perl helper scripts (filter_read_v2.pl, perfect_match_hits_v2.pl, dedup_paired_reads_by_span.pl, umi_v2.pl, umi2_v2.pl). Input: paired-end FASTQ.GZ named R2-1_{TG|TSP|TUr}_rep{1|2}_R1.fastq.gz and _R2.fastq.gz in the run directory. Paths for reference indexes and script directory must be set in the script header to match your environment (see README).