Data accessibility
The grasshopper sequencing data generated here has been deposited on the sequence read archive (SRA) under numbers SRR18000085-SRR18000130. The scripts required to process and analyse these data are available from the GitHub repository https://github.com/SBCSnicholsLab/pseudogene_quantification which also contain an R package called ‘vagrantDNA’ to make available the functions needed to carry out the analysis. The simulation code is available on GitHub repository https://github.com/SBCSnicholsLab/vagrantDnaSim .The SRA identifiers of the human and parrot data used are listed in Supporting Text S1.