Dear PIGA developers,
Thank you for developing this excellent and very useful pipeline. Although PIGA was designed for human genome analyses, I would like to ask whether the framework could theoretically be adapted to other animal species after appropriate customization.
I am currently working on cattle genomics and epigenomics. We have genome assemblies from 13 cattle individuals, including 3 individuals with matched epigenomic data, particularly ATAC-seq. Our main interest is to use personalized or pangenome-aware references to study allele-specific expression and allele-specific regulatory activity, while reducing reference-mapping bias.
I would like to ask whether PIGA could be adapted to such a non-human system if we provide cattle-specific genome assemblies, gene annotations, variant/SV resources, and matched RNA-seq/ATAC-seq data. In particular, I am wondering:
Which parts of PIGA depend on human-specific annotations or resources?
Could these components be replaced by species-specific resources, such as cattle genome assemblies and annotations?
Would the pipeline be suitable for a small set of individuals with high-quality assemblies and matched ATAC-seq data?
Are there any key limitations or assumptions that would make such an adaptation difficult?
I understand that non-human genomes may be outside the current scope of PIGA, but I would greatly appreciate any suggestions or guidance on the feasibility of this direction.
Best regards,
Fuwen Wang
Dear PIGA developers,
Thank you for developing this excellent and very useful pipeline. Although PIGA was designed for human genome analyses, I would like to ask whether the framework could theoretically be adapted to other animal species after appropriate customization.
I am currently working on cattle genomics and epigenomics. We have genome assemblies from 13 cattle individuals, including 3 individuals with matched epigenomic data, particularly ATAC-seq. Our main interest is to use personalized or pangenome-aware references to study allele-specific expression and allele-specific regulatory activity, while reducing reference-mapping bias.
I would like to ask whether PIGA could be adapted to such a non-human system if we provide cattle-specific genome assemblies, gene annotations, variant/SV resources, and matched RNA-seq/ATAC-seq data. In particular, I am wondering:
Which parts of PIGA depend on human-specific annotations or resources?
Could these components be replaced by species-specific resources, such as cattle genome assemblies and annotations?
Would the pipeline be suitable for a small set of individuals with high-quality assemblies and matched ATAC-seq data?
Are there any key limitations or assumptions that would make such an adaptation difficult?
I understand that non-human genomes may be outside the current scope of PIGA, but I would greatly appreciate any suggestions or guidance on the feasibility of this direction.
Best regards,
Fuwen Wang