Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Does accepted_hits.bam include unmapped.bam reads

    Does the accepted_hits.bam file generated by Tophat2 include those placed in unmapped.bam.

    I ask because when I run:
    samtools view accepted_hits.bam | cut -f1 | sort | uniq | wc -l

    And then run:
    cat sample.fq | wc -l
    <result from previous command> / 4

    The two values are exactly the same!

  • #2
    The short answer: nope
    Marco

    Comment


    • #3
      Originally posted by marcowanger View Post
      The short answer: nope
      I'm interested in the long answer. It is too much of a coincidence that these numbers are the same. I'm wanting to get a percentage of mapped reads and unmapped reads of the total number of reads.

      Thanks

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Genetic Variation in Immunogenetics and Antibody Diversity
        by seqadmin



        The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
        11-06-2024, 07:24 PM
      • seqadmin
        Choosing Between NGS and qPCR
        by seqadmin



        Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
        10-18-2024, 07:11 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 11:09 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:13 AM
      0 responses
      23 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 11-01-2024, 06:09 AM
      0 responses
      31 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-30-2024, 05:31 AM
      0 responses
      21 views
      0 likes
      Last Post seqadmin  
      Working...
      X