Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GFF read utility (included as a part of cufflinks)

    From reference genome, if I want to extract sequences based on annotation file in order to create new fasta file,
    does gffread utility exclude intron regions?

    (reference.fasta + annotation.gtf => gffread utility => annotation + exon sequence)

    Thank you in advance.
    Last edited by syintel87; 02-07-2013, 01:07 PM.

  • #2
    Hello, have you done with gffread successfully? I used tophat- cufflinks to analyze my 12 samples, and got a merged.gtf using cuffmerge. I wanted to discard those single exon transcripts and extract the coding sequence and protein sequence. My merged.gtf is 180 Mb and my genome is 280 Mb. I just ran gffread command and I got the gff file and exon sequence using -w argument, but I just got empty cds file and protein file when I used -x and -y argument.
    Did you face this condition?
    Any help is appreciated.
    Best Regards,
    yun

    Comment


    • #3
      I am sorry, but it did not seem to work properly in my case, so that I wrote my own code using python in order to extract CDS from reference genome file.
      Last edited by syintel87; 05-03-2013, 05:44 AM.

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X