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.