Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Couting number of similar reads in sam file and output in bed file

    Hi all,
    Currently, after mapping, I got a sam file which contained approximately 30 million mapped reads. Then, by using bedtool bamtobed, I was able to obtain a bed file. However, there were so many many similar reads.
    Therefore, in order to reduce the size of the final bed file, is there any way that I can mention each read only once as well as its number of presentation in the sam file.

    For instance:

    var_1 0 15 ATGCATGCATGCCGTA
    var_1 0 15 ATGCATGCATGCCGTA
    var_1 0 15 ATGCATGCATGCCGTA
    var_2 5 20 ATGCATGCGGGCCCC

    Will become:
    var_1 0 15 ATGCATGCATGCCGTA 3
    var_2 5 20 ATGCATGCGGGCCCC 1

    Thank you in advance!
    Last edited by bobbyle0210; 11-08-2019, 08:14 PM. Reason: cross-post

  • #2
    Cross-posted and answered on biostars: https://www.biostars.org/p/407019/

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin


      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
      Yesterday, 07:01 AM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    39 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    41 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    35 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    55 views
    0 likes
    Last Post seqadmin  
    Working...
    X