How do I convert Trinity output to GTF/GFF?

[Matt.Ralston]

Hello everyone and thank you for your time,
This is a reiteration of an unanswered question:
TRINITY:Input (Fastq) and Output files (GFF)

How can I convert (FASTA) transcripts produced from Trinity into a GTF/GFF file? I am not interested in alternative workflows for particular things, I just want a GTF/GFF annotation file. Also, I'm not familiar with any long sequence alignment algorithms (would BWA be best??) and a simple conversion to GTF/GFF. Can you please suggest a simple workflow?

[Matt.Ralston]

Answered my own question

Well, since this problem went unanswered, I figured out a way to resolve this issue. It involves all of the things I thought it might, and there may be a simpler way. If you have a better method, please reply so that your solution will be easy to find.

Solution:
bwa-mem of Trinity.fasta to reference genome
samtools -Sbh | bam2bed | bed12ToBed6 | bedToGenePred stdin stdout | genePredToGtf file stdin assembly.gtf

[jp.]

Hi
I have the same problem.
How can I replace Trinity gene numbers to real gene names ?
I have blast hits file from TransDecoder of Trinity.
My question is that how to run DEG to get real gene names, not the Trinity names (Tr1...Trn..)?