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  • How do I convert Trinity output to GTF/GFF?

    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?

  • #2
    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

    Comment


    • #3
      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..)?

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