Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Looking for GTF file of exon annotations (GRCh38/hg38) without success

    Hello, Im new to the site and to be honest, to bioinformatics.

    I will sum it up, im having problems finding the correct file, although I passed the evening checking the forum, github, and other commonly used sources.

    I ended up dling from UCSC a table with exon, but Gene_id and transcript_id isnt giving me the gene names to make a merge with counts, and as far as I have been checking, noone had this issue.

    Code:
    chr1 hg38_knownAlt exon  X1048429  X1048578 X0.000000 X. .
    1 chr1 hg38_knownAlt exon   1048529   1048866         0  + .
    2 chr1 hg38_knownAlt exon  44040072  44040273         0  + .
    3 chr1 hg38_knownAlt exon 155187539 155191999         0  - .
    4 chr1 hg38_knownAlt exon 155189230 155190079         0  - .
    5 chr1 hg38_knownAlt exon 175097494 175117015         0  + .
    6 chr1 hg38_knownAlt exon 197102648 197143690         0  - .
                gene_id.altPromoter..transcript_id.altPromoter.
    1        gene_id bleedingExon; transcript_id bleedingExon; 
    2   gene_id bleedingExon; transcript_id bleedingExon_dup1; 
    3      gene_id strangeSplice; transcript_id strangeSplice; 
    4        gene_id cassetteExon; transcript_id cassetteExon; 
    5 gene_id strangeSplice; transcript_id strangeSplice_dup1; 
    6 gene_id strangeSplice; transcript_id strangeSplice_dup2;
    The parametres I used at UCSC were:
    Clade: Mammal
    Genome: Human
    Assambly: GRCH38/hg38
    track: UCSC Alt Events
    region: whole genome
    output: GTF

    If you could help me I would be grateful, Im not seeing the problem on my petition.

    Thanks in advance.

    GC.
    Beginner @ RNA-Seq, R programming, Linux, Python.-

    Please be patients!

  • #2
    You can get the GTF files you need from GENCODE project here. Multiple options are available so choose what you need. If you truly want to remove other annotations except "exons" then you will need to do a bit of post-processing.
    Last edited by GenoMax; 03-29-2017, 12:05 PM.

    Comment


    • #3
      Thanks you so much, sry for my late answer, I had some personal issues to attend but I got your answer immediatly and was much helpful.

      G.
      Beginner @ RNA-Seq, R programming, Linux, Python.-

      Please be patients!

      Comment


      • #4
        cool broor thankks for sharing.

        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
        12 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