Description of the datasets Data are organized as a folder and compressed with tar.gz. You need to unzip the folder using the command tar -xzvf data.tar.gz. Unzipping will output a folder named data_tidy, which is organized as follow: graph.gfa : Graph in GFA format constructed from 6 cattle assemblies nonref.fa : Non-reference sequences extracted from the graph nonref.fa.masked: Hard masked repetitive regions version of nonref.fa nonref_woflanking.fa: Nonref.fa without flanking sequences nonref_woflanking.fa.masked: Masked version of nonref_woflanking.fa augustus_predict.gtf: Annotated gene models of Augustus from non-ref sequences augustus_prot.fa: Protein fasta of the predicted gene models from Augustus breeds_assembled.gtf: Annotation of the StringTie assembled across-breed transcriptome breeds_expressed.tsv: Expression data of breeds_assembled.gtf de_assembled.gtf: Annotation of the StringTie assembled differentially-expressed transcriptome on non-ref sequences de_expression.tsv: Differential expression results from de_assembled.gtf variant_nonref.tsv: Variants called from non-ref sequences (-1, 0, 1, 2 indicates no call, hom ref, het, and hom alt respectively)