Description

This track shows the transcripts assembled from D. grimshawi Iso-Seq reads by StringTie2. Coding regions within the transcripts are identified by TransDecoder. The Iso-Seq data were obtained from the NCBI Sequence Read Archive under the accession number SRP135764.

Methods

TransDecoder was run against the transcripts assembled by StringTie2 using default parameters. The open reading frames predicted by TransDecoder were searched against the Swiss-Prot database using NCBI blastp and against the Pfam database using HMMER. Open reading frames are kept if they satisfy the TransDecoder.Predict filtering criteria or if they show significant matches to either Swiss-Prot or Pfam.

References

Yang H, Jaime M, Polihronakis M, et al. Re-annotation of eight Drosophila genomes. Life Sci Alliance. 2018;1(6):e201800156. Published 2018 Dec 24. doi:10.26508/lsa.201800156

Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019;20(1):278. Published 2019 Dec 16. doi:10.1186/s13059-019-1910-1

Haas BJ, Papanicolaou A, Yassour M, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494-1512. doi:10.1038/nprot.2013.084