Description

This evidence-based gene annotation track was made from public RNA-seq reads in combination with novel nanopore and PacBio full-length cDNA reads

Methods

Public canine Illumina RNA-seq samples from diverse tissues and breeds was assembled using the superreads module in Stringtie2 and combined with full-length cDNA reads assembled with Stringtie2 and TAMA tools. The best cds for each transcript was identified with TAMA using BLAST hits against the curated Uniprot_Swissprot and ENSEMBL dog annotation v100 protein sequences.

Credits

The gene annotation track was produced as a part of GSD_1.0/CanFam4 reference assembly project by the Lindblad-Toh group of comparative genomics at Uppsala University. Please cite the paper if you use the data for your research.

References

Wang, C.; Wallerman, O.; Arendt, M.-L.; Sundström, E.; Karlsson, Å.; Nordin, J.; Mäkeläinen, S.; Pielberg, G. R.; Hanson, J.; Ohlsson, Å.; Saellström, S.; Rönnberg, H.; Ljungvall, I.; Häggström, J.; Bergström, T. F.; Hedhammar, Å.; Meadows, J. R. S.; Lindblad-Toh, K.
A New Long-Read Dog Assembly Uncovers Thousands of Exons and Functional Elements Missing in the Previous Reference. bioRxiv 2020, 2020.07.02.185108.