Hello all, I have whole genome resequencing data of Brassica napus in fq.gz format (PE). I have checked quality of raw reads, did trimming and alignment using samtools resulted into .bam files. I want to run identify homoeologous exchange including crossing over and non-crossover via read mapping coverage as well BLAST comparisons. I am new to bioinformatics, can anyone guide me with the bash command lines and r script about how I should proceed further.