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equiv_junc_genomes.md

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Example genome and annotations used for equivalent junction analysis in the paper

Human genome (GRCh38)

genome: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh38.primary_assembly.genome.fa.gz

annotation: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz

Mouse genome (mm10)

genome: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/GRCm38.primary_assembly.genome.fa.gz

annotation: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12 /gencode.vM12.annotation.gtf.gz

Rat (rn6)

genome: ftp://ftp.ensembl.org/pub/release-91/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz

annotation: ftp://ftp.ensembl.org/pub/release-91/gtf/rattus_norvegicus/Rattus_norvegicus .Rnor_6.0.91.gtf.gz

Fly (dm3)

genome: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r3.1/fasta

annotation: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r3.1/gff/

Yeast

genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz

annotation: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.gff.gz

Salpingoeca rosetta

genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/695/GCF_000188695.1_Proterospongia_sp_ATCC50818/GCF_000188695.1_Proterospongia_sp_ATCC50818_genomic.fna.gz

annotation: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/695/GCF_000188695.1_Proterospongia_sp_ATCC50818/GCF_000188695.1_Proterospongia_sp_ATCC50818_genomic.gff.gz

Human circRNA

annotation: http://circbase.org/download/hsa_hg19_circRNA.txt

Mouse circRNA

annotation: http://circbase.org/download/mmu_mm9_circRNA.txt