CORAL: Accurate annotation of compact genomes using long-read RNA-seq, demonstrated in Oikopleura dioica (Annotation Files)

GTF files and derived transcriptomic FASTA files for gene annotations created with CORAL for Oikopleura dioica genome.There are files for two O. dioica populations: Berge, Norway (OdiNOR). Barcelona, Spain (OdiBAR). For each population there are a total of 7 files: Odi[...].clean-andOPRNs.gtf: Annotation file that contains all the annotated transcripts. Odi[...]_andOPRNs.fasta: FASTA file generated from the GTF with the same name. Odi[...].clean-noORPNs.counts.gtf: Annotation file that contains all the annotated transcripts excluding operon transcirpts (named 'OPRNs'). Odi[...].clean-noORPNs.counts_longest_trans_only.gtf: Annotation file filtered to only have one transcript per gene, selecting the longest one and exludign operon transcripts. Merge_OPRNs-OpGs_Odi[...].clean.gtf: Annotation file that contains all the operon transcripts and their contained genes (named 'OPRNs' and 'OpGs', respectively). Merge_OPRNs-OpGs_Odi[...].OPRNclean.gtf: Annotation file that contains only the operon transcripts ('OPRNs'). Merge_OPRNs-OpGs_Odi[...].OpGclean.gtf: Annotation file that contains only the genes found to belong to an operon ('OpGs'). The GTF file derived from the SL CAGE data (GEO accesion number GSE50849) is also provided as: GSM1231112_SL_CAGE_trans_splice_sites.named.gtf