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StringTie output to train Augustus

Hi, I ran StringTie and transdecoder. How is it possible to use these outputs as input for Augustus to predict genes with UTR?

Thank you in advance

gene annotation
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written by Ric Ric

Thank you for your link. I also found Incorporating RNA-Seq into AUGUSTUS but they used BLAT. However, I have done all my alignment with HIsat2. Does anyone know how to change the commands to BAM files?

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written by Ric Ric

From Hisat bam file you can run bam2hints

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written by Juke34 Juke34

Thank you, is there a way or necessary to add strand information to the output of bam2hints?

UPDATE:

Bam2hints resutls:

> wc -l .intron-hints.gff 
438503 .intron-hints.gff

.

> head .intron-hints.gff 
NbV1Ch01        b2h     intron  212732  212828  0       .       .       mult=150;pri=4;src=E
NbV1Ch01        b2h     intron  212969  215836  0       .       .       mult=4;pri=4;src=E
NbV1Ch01        b2h     intron  212969  218079  0       .       .       mult=141;pri=4;src=E
NbV1Ch01        b2h     intron  212969  219060  0       .       .       pri=4;src=E
NbV1Ch01        b2h     intron  218387  218908  0       .       .       mult=4;pri=4;src=E
NbV1Ch01        b2h     intron  218387  219060  0       .       .       mult=3;pri=4;src=E
NbV1Ch01        b2h     intron  218671  222563  0       .       .       pri=4;src=E
NbV1Ch01        b2h     intron  218970  219060  0       .       .       mult=4;pri=4;src=E
NbV1Ch01        b2h     intron  219193  219270  0       .       .       pri=4;src=E
NbV1Ch01        b2h     intron  219199  219270  0       .       .       mult=2;pri=4;src=E

In section 3.1 Set hint parameters of this tutorial they asking to adjust the file extrinsic.cfg that holds the hint parameters. However, where is the file located and how to change the settings?

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written by Ric Ric

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