Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • gff2gbSmall

    Hi, everyone.
    I am in trouble converting gff format file to genbank format.

    The gff format file looks like:
    Scaffold_15;HRSCAF=18| StringTie| transcript| 1| 558|1000| .| .| gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "11.043011"; FPKM "0.745167"; TPM "1.132539";
    Scaffold_15;HRSCAF=18| StringTie| exon| 1| 558|1000| .| .| gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "11.043011";

    which is generated by StringTie.

    The command is
    gff2gbSmallDNA.pl stringtie.gff gene.fasta stringtie.gb


    However, I got nothing in stringtie.gb.

    Anyone guys who know why I got an empty file.

    Thanks.

  • #2
    Hi jinfang, I face the same issue you are missing max-size-of-gene-flanking-DNA, gff2gbSmall requires 3 parameters plus the output name <gff-file> <seq-file> and <max-size-of-gene-flanking-DNA> <output-name>

    max-size-of-gene-flanking-DNA: specifies how much DNA is included around genes. The value 0 is fine if you want the output to contain only sequences of coding genes.

    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
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 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
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X