Gene annotation with Augustus

[psahu]

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. It annotates regions as introns while on RNA-seq it is shown as a exon. I have created intron, exonpart hints to feed into augustus but it does not help. Example is shown below.



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

[colindaven]

Try using Maker -which includes augustus - and or gmap with a GFF3 output option.

[psahu]

Try using Maker -which includes augustus - and or gmap with a GFF3 output option.

I am looking for Maker independent options.