Description
This track shows the RNA-Seq transcripts assembled by StringTie. Coding regions
within the transcript are identified by TransDecoder.
TransDecoder was run against the transcripts assembled by StringTie 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
Swiss-Prot or Pfam.
Accession Numbers for RNA-Seq Data
The RNA-Seq data were obtained from NCBI using the following accession numbers:
References
Chen ZX, et al. Comparative validation of
the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014
Jul;24(7):1209-23.
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 Dec 16;20(1):278.
Haas BJ et al. De novo transcript
sequence reconstruction from RNA-Seq using the Trinity platform for reference generation and
analysis. Nat Protoc. 2013 Aug;8(8):1494-512.
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