Header Leaderboard Ad


Can you spot whats wrong with this .gff3?



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

  • Can you spot whats wrong with this .gff3?

    I've been working with tophat for a while pretty successfully, but for some reason this one data set will not cooperate. Using the .gff file I downloaded for the corresponding genome I get:

    [Fri Jul 9 15:45:42 2010] Reading known junctions from GFF file
    Warning: TopHat did not find any junctions in GFF file
    I've tried making several adjustments to the file to make it fit the prescribed format. I've also double checked that the first column matches whats in the bowtie index using bowtie-inspect. Maybe someone else has had a similar experience? I've tried several variants on the following format and nothing helps, which makes me thing is probably something I've overlooked and I am out of ideas.

    Chr01 glean gene 47206323 47208329 . - . ID=BGIOSGA000006;Name=BGIOSGA000006;
    Chr01 glean mRNA 47206323 47208329 0.999993 - . ID=BGIOSGA000006;Name=BGIOSGA000006-TA;Parent=BGIOSGA000006;ID=BGIOSGA000006.50;Name=BGIOSGA000006-TA;ID=BGIOSGA000006;
    Chr01 glean exon 47208026 47208329 . - 0 Parent=BGIOSGA000006;ID=BGIOSGA000006.51;
    Chr01 glean exon 47207590 47207951 . - 2 Parent=BGIOSGA000006;ID=BGIOSGA000006.52;
    Chr01 glean exon 47207158 47207394 . - 0 Parent=BGIOSGA000006;ID=BGIOSGA000006.53;
    Chr01 glean exon 47206323 47206556 . - 0 Parent=BGIOSGA000006;ID=BGIOSGA000006.54;
    Thanks in advance.

Latest Articles


  • seqadmin
    A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
    by seqadmin

    ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

    01-24-2023, 01:19 PM
  • seqadmin
    Introduction to Single-Cell Sequencing
    by seqadmin
    Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

    The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
    01-09-2023, 03:10 PM