Hi @DanielSprockett, thank you for sharing this with me, and for the pun! I tried to recover the original fastq deflines by using fastq-dump --origfmt, but did not find any info there (they were just numbered). After digging around a bit (Original FastQ headers · Issue #130 · ncbi/sra-tools · GitHub) I found out that SRA stopped retaining this information with newer runs. Did you obtain the original read IDs a different way?