Study recombination of the Arabidopsis thaliana radA mutant on cpDNA

For analysis of rearranged sequences, reads properly pairing to the cpDNA were filtered to only keep those showing a short-clipping sequence (threshold 20 nucleotides) and no indel (looking for the presence of an S in the CIGAR string without any I, D and H). The short-clipping sequences were then extracted with SE-MEI/extractSoftclipped (github.com/dpryan79/SE-MEI) and aligned using bowtie2 (Langmead et Salzberg, 2012) against the cpDNA. The positions of the short-clipping sequences mapping the cpDNA and of their relative read were rounded down to the upper kb to analyze the localization of the rearrangement. Those corresponding to the isomerization that results from the recombination involving the large inverted repeats were filtered out.