We made our efforts to utilize existing tools and data resources to avoid reinventing of wheels, standardize the nomenclatures and processes, so that our epi-data analysis can be performed for consistant and uniform outcomes that can be realiably used for comparisons.
Data sources used
- Genome build Bos taurus ARS-UCD1.2: https://ftp.ensembl.org/pub/release-110/fasta/bos_taurus/dna/Bos_taurus.ARS-UCD1.2.dna_sm.toplevel.fa.gz
- Transcriptome GTF file (NCBI – Bos taurus): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/263/795/
- Transcriptome GTF file (Ensembl – Bos taurus): https://ftp.ensembl.org/pub/release-110/gtf/bos_taurus/
- Nextflow/rna-seq code: https://nf-co.re/rnaseq/3.12.0
- NF-core: https://nf-co.re/
- NF-core/rnaseq: https://github.com/nf-core/rnaseq
Tissue ontology references
* All data use at the EpiDB follow the FAANG data sharing statement.