NanoSim pretrained model human_NA12878_dRNA_Bham1_guppy was used to generate transcriptomic reads, stored in file human_NA12878_dRNA_Bham1_guppy_reads.fastq.gz. The modified uLTRA simulators, included in https://github.com/pachterlab/LSRRSRLFKOTWMWMP_2024 Figures folder SupplementaryFigure4, were used to generate: ultra_sim_ONT_homo_2M.fq.gz (2 million ONT InDel Profile reads at 1% sequencing error),ultra_sim_ONT_homo_2M.02.fq.gz (2 million ONT InDel Profile reads at 2% sequencing error),ultra_sim_ONT_homo_2M.04.fq.gz (2 million ONT InDel Profile reads at 4% sequencing error), ultra_sim_PB_homo_2M.001.fq.gz (2 million ONT InDel Profile reads at 0.1% sequencing error),ultra_sim_PB_homo_2M.005.fq.gz (2 million ONT InDel Profile reads at 0.5% sequencing error),ultra_sim_PB_homo_2M.015.fq.gz (2 million ONT InDel Profile reads at 1.5% sequencing error), andultra_sim_PB_homo_2M.02.fq.gz (2 million ONT InDel Profile reads at 2% sequencing error). Lastly, 2 simulation files were not uploaded (due to size of files): Mouse.ONT.R10.4.simulated.shuffled.fastq.gz and human_NA12878_cDNA_Bham1_guppy_reads.fastq.gz. Mouse.PB.simulated.shuffled.fastq.gz and Mouse.ONT.R10.4.simulated.shuffled.fastq.gz are the simulations performed in Prjibelski et al. 2023 (https://doi.org/10.1038/s41587-022-01565-y) that were converted from bams to fastqs with samtools and shuffled with bbtools. NanoSim pretrained model human_NA12878_cDNA_Bham1_guppy was used to generate 10 million transcriptomic reads stored in file human_NA12878_cDNA_Bham1_guppy_reads.fastq.gz.