Genome structural annotation (augustus)

Question

[SP]

Hello all,

I am doing structural gene annotation and using augustus as a tool. While it works quite nicely on most of the cases it shows some miss annotations. One example i shown in the image, as RNA-seq shows that there are no introns present but augustus annotate introns. I have created intron, exonpart hints to feed into augustus but it does not help.

I am looking for any parameter tweaks which can help me get rid of these cases. Every bit of help is appreciated.

My extrinsic file looks like this

   exonpart      1  .992 .985  M    1  1e+100  RM  1     1    E 1    1    W 1    1.05
       exon      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
 intronpart      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
     intron      1        .34  M    1  1e+100  RM  1     1    E 1  1e6    W 1    1
nonexonpart      1          1  M    1  1e+100  RM  1     1.15 E 1    1    W 1    1

Thank you all in advance.

Best regards

Answer 1

[Kay]

have you thought of passing gff file and reads into Maker and training with SNAP

[SP]

Hi @kay, thanks for the input. I am looking for Maker independent solution.