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
have a look here https://github.com/ikmb-denbi/genome-annotation they produce a lot of different evidence to feed Augustus. They have a lot of utilities to produce hints from gtf/gff
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?
From Hisat bam file you can run bam2hints
Thank you, is there a way or necessary to add strand information to the output of bam2hints?
> wc -l .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?
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy