Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • countOverlaps problem

    I have problem using countOverlaps. Below is my code.

    counts=countOverlaps(tx_by_gene,"./s_1_sorted.bam")

    tx_by_gene is a GRangesList object which is a list of GRanges objects, where each GRanges object is a gene and the entries are the genomic coordinates of its transcripts.

    Then I get the error message.

    Error in function (classes, fdef, mtable) :
    unable to find an inherited method for function "countOverlaps", for signature "GRangesList", "character"

    What's wrong in my code? How could I run countOverlaps?

    Thanks,
    Dicty

  • #2
    Hi

    I think you need to load the .bam file by Rsamtools, and use countOverlap after that.




    Originally posted by dicty View Post
    I have problem using countOverlaps. Below is my code.

    counts=countOverlaps(tx_by_gene,"./s_1_sorted.bam")

    tx_by_gene is a GRangesList object which is a list of GRanges objects, where each GRanges object is a gene and the entries are the genomic coordinates of its transcripts.

    Then I get the error message.

    Error in function (classes, fdef, mtable) :
    unable to find an inherited method for function "countOverlaps", for signature "GRangesList", "character"

    What's wrong in my code? How could I run countOverlaps?

    Thanks,
    Dicty

    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