Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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..)?

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Recent Advances in Sequencing Analysis Tools
        by seqadmin


        The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
        05-06-2024, 07:48 AM
      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin




        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
        04-22-2024, 07:01 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 05-14-2024, 07:03 AM
      0 responses
      19 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-10-2024, 06:35 AM
      0 responses
      42 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-09-2024, 02:46 PM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-07-2024, 06:57 AM
      0 responses
      42 views
      0 likes
      Last Post seqadmin  
      Working...
      X