Supporting data for Novel functional sequences uncovered through a bovine multi-assembly graph

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)