No CDS in the novel genes predicted by Isoquant

[sqwwww]

Hi, I'm running Isoquant 3.4.1, I found that the novel genes predicted by Isoquant in Experiment1.extended_annotation.gtf doesn't have CDS information.

Here is my several lines of Experiment1.extended_annotation.gtf :

      1 Chr1    IsoQuant        gene    308327  309241  .       +       .       gene_id "novel_gene_Chr1_100"; transcripts "1"; 
      2 Chr1    IsoQuant        transcript      308327  309241  .       +       .       gene_id "novel_gene_Chr1_100"; transcript_id "transcript99.Chr1.nnic"; exons "
      3 Chr1    IsoQuant        exon    308327  308525  .       +       .       gene_id "novel_gene_Chr1_100"; transcript_id "transcript99.Chr1.nnic"; exon "1"; exon_
      4 Chr1    IsoQuant        exon    308872  309241  .       +       .       gene_id "novel_gene_Chr1_100"; transcript_id "transcript99.Chr1.nnic"; exon "2"; exon_
      5 Chr1    IsoQuant        gene    435395  439640  .       -       .       gene_id "novel_gene_Chr1_484"; transcripts "1"; 
      6 Chr1    IsoQuant        transcript      435395  439640  .       -       .       gene_id "novel_gene_Chr1_484"; transcript_id "transcript483.Chr1.nnic"; exons 
      7 Chr1    IsoQuant        exon    439517  439640  .       -       .       gene_id "novel_gene_Chr1_484"; transcript_id "transcript483.Chr1.nnic"; exon "1"; exon
      8 Chr1    IsoQuant        exon    435395  435667  .       -       .       gene_id "novel_gene_Chr1_484"; transcript_id "transcript483.Chr1.nnic"; exon "2"; exon
      9 Chr1    IsoQuant        gene    436070  437935  .       +       .       gene_id "novel_gene_Chr1_468"; transcripts "2"; 
     10 Chr1    IsoQuant        transcript      436106  437935  .       +       .       gene_id "novel_gene_Chr1_468"; transcript_id "transcript417.Chr1.nnic"; exons 
     11 Chr1    IsoQuant        exon    436106  436394  .       +       .       gene_id "novel_gene_Chr1_468"; transcript_id "transcript417.Chr1.nnic"; exon "1"; exon
     12 Chr1    IsoQuant        exon    436475  436554  .       +       .       gene_id "novel_gene_Chr1_468"; transcript_id "transcript417.Chr1.nnic"; exon "2"; exon
     13 Chr1    IsoQuant        exon    436870  437935  .       +       .       gene_id "novel_gene_Chr1_468"; transcript_id "transcript417.Chr1.nnic"; exon "3"; exon
     14 Chr1    IsoQuant        transcript      436070  437935  .       +       .       gene_id "novel_gene_Chr1_468"; transcript_id "transcript467.Chr1.nnic"; exons 
     15 Chr1    IsoQuant        exon    436070  436554  .       +       .       gene_id "novel_gene_Chr1_468"; transcript_id "transcript467.Chr1.nnic"; exon "1"; exon
     16 Chr1    IsoQuant        exon    436870  437935  .       +       .       gene_id "novel_gene_Chr1_468"; transcript_id "transcript467.Chr1.nnic"; exon "2"; exon
     17 Chr1    IsoQuant        gene    556009  556478  .       -       .       gene_id "novel_gene_Chr1_486"; transcripts "1"; 
     18 Chr1    IsoQuant        transcript      556009  556478  .       -       .       gene_id "novel_gene_Chr1_486"; transcript_id "transcript485.Chr1.nnic"; exons 
     19 Chr1    IsoQuant        exon    556193  556478  .       -       .       gene_id "novel_gene_Chr1_486"; transcript_id "transcript485.Chr1.nnic"; exon "1"; exon
     20 Chr1    IsoQuant        exon    556009  556098  .       -       .       gene_id "novel_gene_Chr1_486"; transcript_id "transcript485.Chr1.nnic"; exon "2"; exon

Is isoquant designed not to provide cds information, or there is something wrong with my process?

[andrewprzh]

Dear @sqwwww

Everything is ok. Current version of IsoQuant does not predict CDS regions and does not copy this information from the input annotation. This might be implemented in one of the future versions.

Best
Andrey