Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • coveragebed output result problem

    Hi,

    I'm running coveragebed to calculate the number of read count in each transcript of tophat alignment result by using the following command:
    Code:
    /bedtool/arq5x-bedtools-26a87ab/bin/coverageBed -abam accepted_hits.bam -b transcripts.bed > transcripts.cov.txt 
    cat transcripts.cov.txt
    gi|224589800|ref|NC_000001.10|  8378168 8404227 "ENSG00000162426"       [B]70      1059    26059   0.0406386[/B]
    Does anybody knows what is the 70, 1059, 26059, 0.0406386 represent?
    I know that 0.0406386 is obtained from 1059/26059.
    Is it 1059 refer to total number of read aligned to the transcript and 26059 represent the transcript length? How about 70?
    Kindly correct me if I'm wrong.
    Thanks for any advice.

  • #2
    If you type "coverageBed -h", the last few lines describe the output format.

    Code:
    Default Output:  
    	 After each entry in B, reports: 
    	   1) The number of features in A that overlapped the B interval.
    	   2) The number of bases in B that had non-zero coverage.
    	   3) The length of the entry in B.
    	   4) The fraction of bases in B that had non-zero coverage.

    Comment


    • #3
      Was looking for this detail

      Thanks alot , very much helped.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      30 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      32 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      28 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Working...
      X