settings for plant genome

[mictadlo]

Hi,
We have a plant genome and would like to create an annotation with Augustus. However, I am not sure about the following few parameters.

• noInFrameStop=false
• allow_hinted_splicesites=atac
• genemodel=partial or --genemodel=complete
• Which settings are appropriate for a plant genome?

Thank you in advance

Michal

[MarioStanke]

I recommend to leave genemodel at the default (partial) for almost all application cases. You don't need to specify it. It may be of use, say, if you want to annotate a specific region only from which you know that it does not truncate a gene.

What splice site patterns occur, depends on the species, and you might find out with spliced alignments of RNA-Seq.
If unsure, I would do
allow_hinted_splicesite=atac
The main ones gtag and gcag are included by default, atac is usually very rare.

noInFrameStop=false makes a GenBank submission easier but may decrease sensitivity, as transcripts with an in-frame stop codon are merely not reported. In-frame stops can only occur whey are spliced and span two exons. The BRAKER pipeline has now a procedure to fix these regions with another option that does not produce in-frame-stops.

[mictadlo]

Thank you.

[mictadlo]

@MarioStanke Just double cheching does noInFrameStop=false or noInFrameStop=true may decrease sensitivity, as transcripts with an in-frame stop codon are merely not reported?

[MarioStanke]

Yes, that is correct. Am Mi., 19. Aug. 2020 um 02:50 Uhr schrieb Michał T. Lorenc < notifications@github.com>:

…

@MarioStanke <https://github.com/MarioStanke> Just double cheching does noInFrameStop=false or noInFrameStop=true may decrease sensitivity, as transcripts with an in-frame stop codon are merely not reported? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#178 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUQQJUBVSVUFJK56LSYB4TSBMOWRANCNFSM4P5LXARQ> .

[mictadlo]

Thank you, but which one noInFrameStop=false or noInFrameStop=true?

[MarioStanke]

noInFrameStop=true produces the subset of transcripts without in-frame stop and therefore may have a lower sensitivity. Am Fr., 21. Aug. 2020 um 09:16 Uhr schrieb Michał T. Lorenc < notifications@github.com>:

…

Thank you, but which one noInFrameStop=false or noInFrameStop=true? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#178 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUQQJW6VUT6N2FEJR7MXJLSBYNODANCNFSM4P5LXARQ> .