Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #16
    I would also be very interested in generating a gtf file for arabidopsis. Would it be possible to post the code ?

    Comment


    • #17
      Download TAIR10_GFF3_genes.gff inTAIR, and then use the Perl script below to convert this gff file to gtf which is used as conference annotation Cufflinks.

      #!/usr/bin/perl

      use warnings;
      use strict;
      while (<>) {
      chomp;
      my @parts = split /\t/;
      if ( !(($parts[2] eq 'three_prime_UTR')|($parts[2] eq 'five_prime_UTR')|($parts[2] eq 'exon')|($parts[2] eq 'CDS')) ) {
      next;
      }
      elsif ( $parts[2] eq 'three_prime_UTR') {
      $parts[2] = '3UTR';
      }
      elsif ($parts[2] eq 'five_prime_UTR') {
      $parts[2] = '5UTR';
      }
      $parts[8] =~ s/^Parent=((\w+)\.\w*).*/gene_id \"$2\"; transcript_id \"$1\";/sg;
      $_ = join "\t" , @parts;
      print "$_\n";
      }

      Comment


      • #18
        celeste8, thank you very much !

        Comment


        • #19
          Thanks, celeste8!!
          Sam Hokin
          Computational Scientist, Carnegie and NCGR

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM
          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 06:37 PM
          0 responses
          8 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          8 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          49 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          66 views
          0 likes
          Last Post seqadmin  
          Working...
          X